http://wiki.docking.org/api.php?action=feedcontributions&user=Jklyu&feedformat=atomDISI - User contributions [en]2024-03-28T10:08:59ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Generating_decoys_(Reed%27s_way)&diff=14838Generating decoys (Reed's way)2022-09-22T23:41:08Z<p>Jklyu: /* Step 2) Retrieving SMILES decoys from ZINC15 */</p>
<hr />
<div>Written by Reed Stein on April 3, 2018.<br />
<br />
updated 5/3/2019<br />
<br />
updated 8/15/2019<br />
<br />
updated 3/6/2020<br />
<br />
updated 5/18/2020<br />
<br />
This pipeline will generate property-matched decoys for a set of ligand SMILES. To build ligands yourself, see "ligand prep" in:<br />
http://wiki.docking.org/index.php/DOCK_3.7_tutorial_%28Anat%29<br />
<br />
All scripts for this tutorial can be found in:<br />
/mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/<br />
<br />
Before running any scripts, make sure to source the current version of Python<br />
source /nfs/soft/python/envs/complete/current/env.csh<br />
<br />
Additionally, JChem needs to be sourced in your ~/.cshrc file with the command:<br />
source /nfs/soft/jchem/current/env.csh<br />
<br />
If the below script still not run:<br />
source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br />
== Querying ZINC for Protomers ==<br />
<br />
This procedure generates decoys for your input ligands by searching through 3D conformers that are already built in ZINC. This procedure is advised if you want decoys to be charge-matched to ligands.<br />
<br />
=== Step 1) Setting up directories for Protomers ===<br />
<br />
Before starting, you need a SMILES file with the format (SMILES first, <B>unique</B> ID second):<br />
S(Nc1c(O)cc(C(=O)O)cc1)(c2c(scc2)C(=O)O)(=O)=O 116<br />
<br />
You also need an input file named "decoy_generation.in" with the following lines:<br />
<br />
PROTONATE YES<br />
MWT 0 125<br />
LOGP 0 3.6<br />
RB 0 5<br />
HBA 0 4<br />
HBD 0 3<br />
CHARGE 0 2<br />
LIGAND TC RANGE 0.0 0.35<br />
MINIMUM DECOYS PER LIGAND 20<br />
DECOYS PER LIGAND 50<br />
MAXIMUM TC BETWEEN DECOYS 0.8<br />
TANIMOTO YES<br />
<br />
<br />
If your input ligand SMILES file is already protonated as you want it, set "PROTONATE NO". <br />
<br />
If you want your input ligand SMILES protonated, only protomer SMILES with unique properties will be kept for generating decoys. Therefore, if you have one ligand that exists in 4 tautomers, all of which have identical molecular weight, cLogP, # rotatable bonds, # H-bond acceptors and donors, and net charge, only <B>one</B> will be maintained for decoy matching. This doesn't apply if you set "PROTONATE NO".<br />
<br />
This file specifies that for each ligand protomer, at least 20 decoys will be retrieved with the following properties:<br />
- within +/- 125 Daltons<br />
- within +/- 3.6 logP<br />
- within +/- 5 rotatable bonds<br />
- within +/- 4 hydrogen bond acceptors<br />
- within +/- 3 hydrogen bond donors<br />
- within +/- 2 charge<br />
- 0.35 or less Tanimoto<br />
- minimum 20 decoys per ligand protomer, if available<br />
- preferred 50 decoys per ligand protomer, if available<br />
- the maximum TC between decoy molecules should be 0.8<br />
- "TANIMOTO" refers to whether a Tanimoto calculation should be performed - see step 3 for when this is necessary<br />
<br />
These are <B>arbitrary</B>, and you can input your desired minimum and maximum values that decoys can differ by, relative to the ligands. <br />
<br />
Once you have created this file, run the following command to create the decoy generation directory:<br />
<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0000_protonate_setup_dirs.py {SMILES_FILE} {NEW_DIR_NAME}<br />
<br />
Provide a directory name that you want in place of {NEW_DIR_NAME}. This will create the directory with subdirectories named<br />
"ligand_${number}" for each of the ligands in the SMILES file you input.<br />
<br />
=== Step 2) Retrieving protomer decoys from ZINC15 ===<br />
<br />
If you have edited the "decoy_generation.in" file which is now located in {NEW_DIR_NAME} as you want, you can run the following command:<br />
<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0001_qsub_generate_decoys.py {NEW_DIR_NAME}<br />
<br />
This should take 15 minutes to an hour, depending on how many ligands you input.<br />
<br />
=== Step 3) Assigning accepted protomer decoys to each ligand protomer ===<br />
<br />
We can assign the property-matched decoys to the ligand protomers. Make sure you have the "decoy_generation_input.in" file from before in {NEW_DIR_NAME}. <br />
<br />
To filter the decoys, run the following command:<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0002_qsub_filter_decoys.py {NEW_DIR_NAME}<br />
<br />
This will run on the queue. A log file called "FILTER_DECOYS.log" will be generated in {NEW_DIR_NAME} with information and any errors.<br />
<br />
If you don't get enough decoys, the "decoy_generation.in" file can be modified by changing "MAXIMUM TC BETWEEN DECOYS", "MINIMUM DECOYS PER LIGAND", etc.<br />
To not run the time-consuming Tanimoto calculation between all decoys again, simply add/change this in the "decoy_generation.in" file:<br />
<br />
TANIMOTO NO<br />
<br />
If you set Tanimoto to "NO", make sure that your {NEW_DIR_NAME} still has the original files:<br />
<br />
"test_ligdecoy_smiles.smi"<br />
"cluster_head.list"<br />
<br />
Otherwise, this step will not run.<br />
<br />
If these original files still remain, this will skip the Tanimoto calculation step, and filter property matched decoys based on the new parameters in the "decoy_generation.in" file.<br />
<br />
If this has completed successfully, you should see files in your {NEW_DIR_NAME} with the format "{LIGAND_ID}_final_property_matched_decoys.txt". These files contain the ligands and their properties, as well as property-matched decoys that have been assigned to them. These files have the format "SMILES", "ZINC ID", "logP", "#Rotatable Bonds", "# Hydrogen Bond Donors", "# Hydrogen Bond Acceptors", "Charge", "Protomer SMILES", and "Tanimoto Coefficient to Ligand".<br />
<br />
There should also be files with the format "{LIGAND_ID}_replacements.txt", which include extra property-matched decoys that were assigned to that ligand. <br />
<br />
If you still cannot get enough decoys for your ligands, consider reducing the number of ligands you have by clustering, for example, or using the SMILES decoy generation below, which is not limited to only molecules that are already built in ZINC15.<br />
<br />
=== Step 4) Copying decoy .db2.gz files into your directories ===<br />
<br />
To copy property-matched decoys into your own directory of choice, run the following command:<br />
<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0003_copy_decoys_to_new_dir.py {NEW_DIR_NAME} {COPY_TO_DIR}<br />
<br />
where {COPY_TO_DIR} is a new directory that will be created where your decoys will be copied into. In this directory, two subdirectories will be created:<br />
"ligands" - this includes the input ligands for which there are X number property matched decoys (these are all ligands with "{LIGAND_ID}_final_property_matched_decoys.txt" files in {NEW_DIR_NAME})<br />
"decoys" - this will include the decoy .db2.gz files for docking and "decoys.smi" which contains all the SMILES strings for property matched decoys<br />
<br />
IMPORTANT: It is possible that all of your ligand protomers were not matched to property-matched decoys. The "ligands.smi" file in {COPY_TO_DIR} will not include these. Make <br />
sure you do not dock these if you calculate enrichment values.<br />
<br />
== Querying ZINC for SMILES ==<br />
<br />
This procedure generates decoys for your input ligand SMILES by finding decoy SMILES in ZINC that are property-matched. This procedure will provide decoy SMILES that you can build yourself into 3D models for docking. If you would like to query ZINC for decoy SMILES so that you can build decoys yourself or if your ligands are >400 Da, start here. If not, go to "Querying ZINC for Protomers" to generate decoys that already have 3D models.<br />
<br />
=== Step 1) Setting up SMILES directory ===<br />
<br />
Before starting, you need a SMILES file with the format (SMILES first, ID second):<br />
S(Nc1c(O)cc(C(=O)O)cc1)(c2c(scc2)C(=O)O)(=O)=O 116<br />
<br />
You also need an input file named "decoy_generation.in" with the following lines:<br />
<br />
SMILES YES<br />
PROTONATE YES<br />
MWT 0 125<br />
LOGP 0 3.6<br />
RB 0 5<br />
HBA 0 4<br />
HBD 0 3<br />
CHARGE 0 2<br />
LIGAND TC RANGE 0.0 0.35<br />
MINIMUM DECOYS PER LIGAND 20<br />
DECOYS PER LIGAND 50<br />
MAXIMUM TC BETWEEN DECOYS 0.8<br />
TANIMOTO YES<br />
GENERATE DECOYS 750<br />
<br />
If your input ligand SMILES file is already protonated as you want it, set "PROTONATE NO". "SMILES" tells the function you want to query ZINC for SMILES, not built protomers.<br />
<br />
This file specifies that for each ligand protomer, {MINIMUM DECOYS PER LIGAND} to {DECOYS PER LIGAND} decoys will be retrieved with the following properties:<br />
- within +/- 125 Daltons<br />
- within +/- 3.6 logP<br />
- within +/- 5 rotatable bonds<br />
- within +/- 4 hydrogen bond acceptors<br />
- within +/- 3 hydrogen bond donors<br />
- within +/- 2 charge<br />
- 0.35 or less Tanimoto<br />
<br />
"GENERATE DECOYS" specifies how many potential decoys you want to check for property matching with your ligands. A smaller number results in faster decoy generation, but a smaller pool of potential decoys to compare your ligand against. A larger number results in slower decoy generation, and greater likelihood of property-matched decoys for all your ligands. <br />
<br />
As with protomers, "MINIMUM DECOYS PER LIGAND" refers to the minimum number of decoys you want for each ligand protomer; <br />
<br />
"DECOYS PER LIGAND" refers to your preferred number of decoys for each ligand protomer;<br />
<br />
"MAXIMUM TC BETWEEN DECOYS" refers to the maximum Tc allowed between decoys (the lower, the more dissimilar your decoys will be);<br />
<br />
and "TANIMOTO" refers to whether the ligand-decoy full Tc matrix should be calculated - this must be done at least once and should not be set to "NO" unless you are re-running step 3.<br />
<br />
<br />
These are <B>arbitrary</B>, and you can input your desired minimum and maximum values that decoys can differ by, relative to the ligands. <br />
<br />
Once you have created this file, run the following command to create the decoy generation directory:<br />
<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0000_protonate_setup_dirs.py {SMILES_FILE} {NEW_DIR_NAME}<br />
<br />
Provide a directory name that you want in place of {NEW_DIR_NAME}. This will create the directory with subdirectories named<br />
"ligand_${number}" for each of the ligands in the SMILES file you input.<br />
<br />
=== Step 2) Retrieving SMILES decoys from ZINC15 ===<br />
<br />
If you have edited the "decoy_generation.in" file which is now located in {NEW_DIR_NAME} as you want, you can run the following command:<br />
<br />
python /mnt/nfs/ex9/work/stefan/Covid-19/20210804_Mpro_CUBS/decoys_larger_SMILES/test-code/0001_qsub_generate_decoys.py {NEW_DIR_NAME}<br />
<br />
Jobs will run for 15 minutes to 1-2 hours depending on how many ligands you input.<br />
<br />
=== Step 3) Assigning decoys to ligands ===<br />
<br />
To assign property matched decoys to your ligand protomers, run the following command:<br />
<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0002_qsub_filter_decoys.py {NEW_DIR_NAME}<br />
<br />
This will run on the queue. As with "Querying ZINC for Protomers": <br />
<br />
If you don't get enough decoys, the "decoy_generation.in" file can be modified by changing "MAXIMUM TC BETWEEN DECOYS", "MINIMUM DECOYS PER LIGAND", etc.<br />
To not run the time-consuming Tanimoto calculation between all ligands and decoys again, simply add/change this in the "decoy_generation.in" file:<br />
<br />
TANIMOTO NO<br />
<br />
If you set Tanimoto to "NO", make sure that your {NEW_DIR_NAME} still has the original files:<br />
<br />
"test_ligdecoy_smiles.smi"<br />
"cluster_head.list"<br />
<br />
Otherwise, this step will not run.<br />
<br />
If these original files still remain, this will skip the Tanimoto calculation step, and filter property matched decoys based on the new parameters in the "decoy_generation.in" file.<br />
<br />
If this has completed successfully, you should see files in your {NEW_DIR_NAME} with the format "{LIGAND_ID}_final_property_matched_decoys.txt". These files have the format "SMILES", "ZINC ID", "logP", "#Rotatable Bonds", "# Hydrogen Bond Donors", "# Hydrogen Bond Acceptors", "Charge", "Protomer ID", and "Tanimoto Coefficient to Ligand".<br />
<br />
These files contain the ligands and their properties, as well as property-matched decoys that have been assigned to them. There should also be files with the format "{LIGAND_ID}_replacements.txt", which include extra property-matched decoys that were assigned to that ligand.<br />
<br />
=== Step 4) Setting up ligand/decoy directories for building SMILES ===<br />
<br />
If you have queried ZINC for SMILES, you need to build the decoys yourself. To write the SMILES file, run the following command:<br />
<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0003b_write_out_ligands_decoys.py {NEW_DIR_NAME} {COPY_TO_DIR}<br />
<br />
This will create {COPY_TO_DIR} with two subdirectories, "ligands" and "decoys" as well as SMILES files for:<br />
<br />
ligands.smi - this includes the input ligands for which there are X number property matched decoys (these are all ligands with "{LIGAND_ID}_final_property_matched_decoys.txt" files in {NEW_DIR_NAME})<br />
decoys.smi - this includes the canonicalized property-matched decoy SMILES<br />
decoy_protomers.smi - this includes the actual property-matched decoy protomer SMILES<br />
<br />
SMILES for decoys can now be built.<br />
<br />
For decoy building, use the following command:<br />
<br />
setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk<br />
source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br />
${DOCKBASE}/ligand/generate/build_database_ligand.sh -H $ph decoy_protomers.smi <B>--pre-tautomerized</B> --no-db<br />
<br />
If not all decoys successfully build, more property matched decoys can be taken from the "{LIGAND_ID}_replacements.txt" files. Additionally, you can build decoys without the <B>--pre-tautomerized</B> flag:<br />
<br />
${DOCKBASE}/ligand/generate/build_database_ligand.sh -H $ph <B>decoys.smi</B> --no-db<br />
<br />
This will produce all protomers of each decoy, including the property-matched decoy protomer.<br />
<br />
== Visualizing Decoy Properties ==<br />
=== Visualizing property distributions ===<br />
<br />
To visualize the distributions of molecular properties of matched decoys relative to the ligands, run the following command:<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0004_plot_properties.py {NEW_DIR_NAME}<br />
<br />
There will be 6 images in {NEW_DIR_NAME} for molecular weight, logP, number of rotatable bonds, number of hydrogen bond donors, number of hydrogen bond acceptors, and net charge of ligands and decoys.<br />
<br />
=== Visualizing decoy Tanimotos to ligands ===<br />
<br />
To visualize how different the matched decoys are to the input ligands, run the following command:<br />
python /mnt/nfs/home/rstein/zzz.scripts/new_DUDE_SCRIPTS/0005_plot_tanimoto_to_lig.py {NEW_DIR_NAME}<br />
<br />
There will be a box and whisker plot image in {NEW_DIR_NAME} showing the Tanimotos calculated between each ligand and all decoys.</div>Jklyuhttp://wiki.docking.org/index.php?title=AWS:Merge_and_download_results&diff=14361AWS:Merge and download results2022-06-29T19:23:56Z<p>Jklyu: </p>
<hr />
<div>[[Category:AWS DOCK]]<br />
<br />
=== Prerequisites ===<br />
<br />
github personal access token & DOCK repository access rights (https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)<br />
<br />
aws account & credentials (https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html#access-keys-and-secret-access-keys)<br />
<br />
=== Step 1: Create an EC2 instance ===<br />
<br />
Go to AWS dashboard, look up EC2 in the search bar and click the link.<br />
<br />
Navigate to "instances" tab and select "Launch Instance"<br />
<br />
[[File:Launchinstances.png|frameless]]<br />
<br />
For Instance Type, find an instance appropriate for your analysis workload. You can't go wrong with more vCPUs and Memory, so a t2.xlarge or t2.2xlarge will work just fine for just about any workload.<br />
<br />
[[File:Instancetype.png|frameless]]<br />
<br />
Word to the wise: if you're going to allocate an expensive instance, MAKE SURE NOT TO FORGET ABOUT IT! You don't want a surprise 1000$ bill at the end of the month for an instance you barely used.<br />
<br />
Next, create a new key pair for your instance. Use RSA encryption and give it a descriptive name, making sure to save the .pem or .ppk file somewhere you will remember it. This key can be re-used for any additional instances you create in the future.<br />
<br />
[[File:Keypair.png|frameless]]<br />
<br />
Finally, configure the storage available to your instance. Depending on how many poses your docking run produced, you may want just a few GB, or a few TB.<br />
<br />
[[File:Configstorage.png|frameless]]<br />
<br />
Now launch your instance, this will bring you to a page showing your instance's ID. Click on that ID to view the details of your instance.<br />
<br />
[[File:Instancelaunched1.png|frameless]]<br />
<br />
[[File:Instancelaunched2.png|frameless]]<br />
<br />
[[File:Instancelaunched3.png|frameless]]<br />
<br />
=== Step 2: Connect to your EC2 instance and install required software ===<br />
<br />
In your instance's details page, find it's public ipv4 address.<br />
<br />
Using your preferred ssh client, connect to your instance. The default username on ec2 instances is ec2-user, meaning your ssh command should look as follows:<br />
<nowiki><br />
ssh -i /path/to/my/key.pem ec2-user@54.221.XXX.XXX</nowiki><br />
<br />
Once logged in to your instance, you will need to install all dependencies:<br />
<br />
* git<br />
* DOCK<br />
* python3.8<br />
<br />
git:<br />
<nowiki><br />
sudo yum install git</nowiki><br />
<br />
DOCK:<br />
<nowiki><br />
git clone https://github.com/docking-org/DOCK.git</nowiki><br />
<br />
python3.8:<br />
<nowiki><br />
sudo amazon-linux-extras enable python3.8<br />
sudo yum install python3.8</nowiki><br />
<br />
=== Step 3: Configure AWS, Copy data from S3 ===<br />
<br />
First, configure your aws credentials.<br />
<br />
<nowiki><br />
~$ aws configure<br />
AWS Access Key ID [None]: MY_ACCESS_KEY<br />
AWS Secret Access Key [None]: MY_SECRET_ACCESS_KEY<br />
Default region name [None]: us-west-1<br />
Default output format [None]:</nowiki><br />
<br />
Enter your access keys, and the region you ran docking in. Leave output format blank (or don't, it really doesn't matter).<br />
<br />
Find the location where DOCK wrote output to in your S3 bucket, e.g<br />
<br />
<nowiki><br />
~$ aws s3 ls s3://btingletestbucket/docking_runs/5HT2A/H17/<br />
PRE aa/<br />
PRE ab/<br />
~$ aws s3 ls s3://btingletestbucket/docking_runs/5HT2A/H17/aa/<br />
PRE 1/<br />
PRE 2/<br />
...<br />
PRE 10000/<br />
~$ aws s3 ls s3://btingletestbucket/docking_runs/5HT2A/H17/aa/1/<br />
2021-03-16 22:50:57 2111052 OUTDOCK.0<br />
2021-03-16 22:50:58 4705515 test.mol2.gz.0</nowiki><br />
<br />
Copy all the results you want to analyze to your instance. You don't need OUTDOCK to do analysis any more, so you can save on transfer fees by excluding them from the copy, like so:<br />
<br />
<nowiki><br />
~$ mkdir -p data/5HT2A/H17<br />
~$ aws s3 cp --recursive --exclude "*OUTDOCK.gz*" s3://btingletestbucket/docking_runs/5HT2A/H17 data/5HT2A/H17<br />
(lots of copy logs)<br />
~$ ls data/5HT2A/H17<br />
aa ab</nowiki><br />
<br />
=== Step 4: Run Analysis and save results ===<br />
<br />
All that's left to do is run analysis using the new [[Docking_Analysis_in_DOCK3.8#top_poses.py|top_poses.py]] script. <br />
<br />
<nowiki><br />
python3.8 ~/DOCK/ucsfdock/analysis/top_poses/top_poses.py ~/data/5HT2A/H17 -n 10000 -o ~/data/5HT2A/poses_H17 -j 1</nowiki><br />
<br />
There is no need to provide a dirlist, top_poses.py will find all test.mol2* files beneath the directory you specify. Alternatively you can provide a text file containing a list of test.mol2* files to analyze.<br />
<br />
Two files will be created, a .mol2.gz file and a .scores file. The .mol2.gz file will contain the mol2 data for all top poses, and .scores will contain a text line for each top pose describing energy etc parameters.<br />
<br />
You can copy these output files to your S3 bucket, or use SCP to copy them to your computer. <br />
<br />
<nowiki><br />
scp -i /path/to/my/key.pem ec2-user@XXX.XXX.XXX.XXX:~/data/5HT2A/H17/poses_H17.mol2.gz poses_H17.mol2.gz</nowiki><br />
<br />
IMPORTANT:<br />
<br />
Once you're done, make sure to terminate the instance in your EC2 console. Be aware that any data on your instance will be deleted when you do this, so copy back anything you care about first.<br />
<br />
[[File:Terminateinstance.png|frameless]]</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14146Coloring and Subcluster Matching2022-04-12T20:37:25Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
The colored matching spheres should look like the example below. If you are not satisfied with the color code combination generated by the automatic way, you should be able to change them based the tutorial in this section. The last column of each matching sphere is a number that you can interpret based on the color code table provided in this section, so you can easily change the last number in each line (each matching sphere) based on the color code table to customize your color code combination.<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
The color code table for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14145Coloring and Subcluster Matching2022-04-12T20:37:02Z<p>Jklyu: /* Manual way to modify colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
The colored matching spheres should look like the example below. If you are not satisfied with the color code combination generated by the automatic way, you should be able to change them based the tutorial in this section. The last column of each matching sphere is a number that you can interpret based on the color code table provided in this section, so you can easily change the last number in each line (each matching sphere) based on the color code table to customize your color code combination.<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
The color code table for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14144Coloring and Subcluster Matching2022-04-12T20:31:51Z<p>Jklyu: /* Manual way to modify colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
The colored matching spheres should look like the example below. If you are not satisfied with the color code combination generated by the automatic way, you should be able to change them based the tutorial in this section. The last column of each matching sphere is a number that you can interpret based on the color code table provided in this section, so you can easily change the last number in each line (each matching sphere) based on the color code table to customize<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
The color code table for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14143Coloring and Subcluster Matching2022-04-12T19:46:38Z<p>Jklyu: /* Manual way to modify colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
The colored matching spheres should look like the example below. If you are not satisfied with the color code combination generated by the automatic way, you should be able to change them based the tutorial in this section. The last column of each matching sphere is a number that you can interpret based on the color code table provided in this section, so you can easily change the last number in each line (each matching sphere) based on the color code table. <br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
The color code table for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14142Coloring and Subcluster Matching2022-04-12T19:38:12Z<p>Jklyu: /* Manual way to modify colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
The colored matching spheres should look like the example below. The last column of each matching sphere is a number that you can interpret based on the color code table provided in this section<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
The color code table for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14141Coloring and Subcluster Matching2022-04-12T19:36:38Z<p>Jklyu: /* Manual way to modify colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
The colored matching spheres should look like the example below. The last column of each matching sphere is a number that you can interpret based on the color code table provided in this section<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14140Coloring and Subcluster Matching2022-04-12T19:20:14Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022. Color and subcluster matching is a new feature that is only available in DOCK3.8<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14139Coloring and Subcluster Matching2022-04-12T17:40:24Z<p>Jklyu: /* Manual way to modify colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
cluster 1 number of spheres in cluster 50<br />
1 44.17800 39.27200 32.01900 0.700 1 0 1<br />
5 49.92100 42.48100 40.14300 0.700 5 0 2<br />
7 44.01400 39.64100 40.42600 0.700 7 0 3<br />
13 42.63200 39.82900 36.02200 0.700 13 0 4<br />
15 47.34200 41.02400 42.26600 0.700 15 0 7<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14138Coloring and Subcluster Matching2022-04-12T16:33:34Z<p>Jklyu: /* Generate colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Automatic way to generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Manual way to modify colored matching spheres ===<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14137Coloring and Subcluster Matching2022-04-12T16:32:35Z<p>Jklyu: /* Automatic way to generate colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14136Coloring and Subcluster Matching2022-04-12T16:32:07Z<p>Jklyu: /* Generate colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022.<br />
<br />
== Automatic way to generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=14135Coloring and Subcluster Matching2022-04-12T16:29:04Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13474Coloring and Subcluster Matching2021-04-12T20:33:26Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
#####################################################<br />
# MATCHING<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13473Coloring and Subcluster Matching2021-04-12T20:32:44Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
k_clusters 1<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13460Coloring and Subcluster Matching2021-03-31T22:44:28Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13459Coloring and Subcluster Matching2021-03-31T22:43:30Z<p>Jklyu: /* Generate clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl INDOCK<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13458Coloring and Subcluster Matching2021-03-31T22:41:58Z<p>Jklyu: /* Generate clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK_cl .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13457Coloring and Subcluster Matching2021-03-31T22:41:46Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp INDOCK INDOCK_cl<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13456Coloring and Subcluster Matching2021-03-31T22:40:58Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
cp <br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13455Coloring and Subcluster Matching2021-03-31T22:39:20Z<p>Jklyu: /* Create a directory and copy necessary files from your original receptor preparation folders */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK .<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13454Coloring and Subcluster Matching2021-03-31T22:37:34Z<p>Jklyu: /* Analyze your enrichment calculations */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
# I will revisit this part when I have time<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13453Coloring and Subcluster Matching2021-03-31T22:37:09Z<p>Jklyu: /* Analyze your enrichment calculations */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==<br />
cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}<br />
# you have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method<br />
csh analysis.csh</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13452Coloring and Subcluster Matching2021-03-31T22:31:32Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/<br />
<br />
== Analyze your enrichment calculations ==</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13451Coloring and Subcluster Matching2021-03-31T22:29:33Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
== Submit enrichment calculations ==<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13450Coloring and Subcluster Matching2021-03-31T22:28:21Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate<br />
<br />
=== Submit enrichment calculations ===<br />
cd ${workdir}<br />
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count<br />
cp /where you store ligands and decoys/ligands-decoys.sdi .<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13449Coloring and Subcluster Matching2021-03-31T22:25:49Z<p>Jklyu: /* Generate clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
conda activate ClusterDOCK<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m<br />
conda deactivate</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13448Coloring and Subcluster Matching2021-03-31T22:24:49Z<p>Jklyu: /* Generate colored and clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Install a conda environment to generate clustered matching spheres ===<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml<br />
For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13447Coloring and Subcluster Matching2021-03-31T22:20:42Z<p>Jklyu: /* Generate clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp ${workdir}/INDOCK .<br />
cp ../../dockfiles . -r<br />
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph<br />
<br />
conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13446Coloring and Subcluster Matching2021-03-31T22:17:52Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
Add the section below if you want to explore subcluster matching as well<br />
#####################################################<br />
# DOCKING<br />
docking_mode 4<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp INDOCK .</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13445Coloring and Subcluster Matching2021-03-31T22:16:24Z<p>Jklyu: /* Generate clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
mkdir cluster_spheres<br />
cd cluster_spheres<br />
mkdir meta<br />
cd meta<br />
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi<br />
cp /where you store ligands and decoys/ligands.name ligands.names<br />
cp /where you store ligands and decoys/decoys.name decoys.names<br />
cp INDOCK .</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13444Coloring and Subcluster Matching2021-03-31T22:12:58Z<p>Jklyu: /* Generate colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
cp matching_spheres.cl.red.sph dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13443Coloring and Subcluster Matching2021-03-31T22:12:00Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.red.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13442Coloring and Subcluster Matching2021-03-31T22:11:43Z<p>Jklyu: /* Generate colored matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13441Coloring and Subcluster Matching2021-03-31T22:10:37Z<p>Jklyu: /* Source my DOCKBASE */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Generate clustered matching spheres ===<br />
cd ${workdir}<br />
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13440Coloring and Subcluster Matching2021-03-31T22:09:24Z<p>Jklyu: /* Source my DOCKBASE */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Source my DOCKBASE ===<br />
cd ${workdir}</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13439Coloring and Subcluster Matching2021-03-31T22:08:56Z<p>Jklyu: /* Generate colored and clustered matching spheres */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Source my DOCKBASE ===<br />
cd</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13438Coloring and Subcluster Matching2021-03-31T22:07:02Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK<br />
<br />
== Generate colored and clustered matching spheres ==<br />
<br />
=== Source my DOCKBASE ===</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13437Coloring and Subcluster Matching2021-03-31T22:06:15Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== Source my DOCKBASE ===<br />
Since all of these is still in the development stage, you have to use my dev branch to run docking calculations<br />
setenv DOCKBASE /mnt/nfs/home/jklyu/zzz.github/DOCK3/DOCK</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13436Coloring and Subcluster Matching2021-03-31T21:58:16Z<p>Jklyu: /* Create a directory and copy necessary files from your original receptor preparation folders */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folder/dockfiles . -r<br />
cp /your receptor preparation folder/INDOCK INDOCK_ori<br />
cp /your receptor preparation folder/xtal-lig.pdb .<br />
cp /your receptor preparation folder/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== ===</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13435Coloring and Subcluster Matching2021-03-31T21:56:07Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
<br />
Add the section below into your INDOCK file<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph<br />
<br />
=== ===</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13434Coloring and Subcluster Matching2021-03-31T21:53:10Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13433Coloring and Subcluster Matching2021-03-31T21:49:55Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13432Coloring and Subcluster Matching2021-03-31T21:48:56Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
The first column of a match means the color code from the ligand atom and the second column means the color code from the corresponding matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13431Coloring and Subcluster Matching2021-03-31T21:45:01Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
The color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
The color codes for atoms in the rigid fragment in db2 files<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
# The first column shows<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13430Coloring and Subcluster Matching2021-03-31T20:24:06Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
color codes for matching spheres <br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
# The first column shows<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13429Coloring and Subcluster Matching2021-03-31T19:34:48Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
<br />
<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
# The first column shows<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure your INDOCK parameter points to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13428Coloring and Subcluster Matching2021-03-31T19:34:10Z<p>Jklyu: </p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
<br />
<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
# The first column shows<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure you point to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyuhttp://wiki.docking.org/index.php?title=Coloring_and_Subcluster_Matching&diff=13427Coloring and Subcluster Matching2021-03-31T19:32:53Z<p>Jklyu: /* Prepare your INDOCK file for color matching */</p>
<hr />
<div>Written by Jiankun Lyu on March 31st, 2021.<br />
<br />
== Generate colored matching spheres ==<br />
<br />
=== Create a directory and copy necessary files from your original receptor preparation folders ===<br />
<br />
set workdir = /where you want to run your coloring and subcluster matching/<br />
mkdir -p ${workdir}<br />
cd ${workdir}<br />
cp /your receptor preparation folders/dockfiles . -r<br />
cp /your receptor preparation folders/INDOCK INDOCK_ori<br />
cp /your receptor preparation folders/xtal-lig.pdb .<br />
cp /your receptor preparation folders/working/rec.crg.pdb .<br />
cd dockfiles<br />
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb<br />
<br />
=== Generate colored matching spheres ===<br />
<br />
cd ../<br />
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"<br />
cp matching_spheres.cl.sph ../dockfiles<br />
<br />
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.<br />
<br />
=== Prepare your INDOCK file for color matching ===<br />
<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
not_neutral (8)<br />
positive_or_donor (9)<br />
negative_or_acceptor (10)<br />
neutral_or_acceptor_or_donor (11)<br />
donacc (12)<br />
positive_or_acceptor (13)<br />
negative_or_donor (14)<br />
negative_or_acceptor_or_donor (15)<br />
positive_or_acceptor_or_donor (16)<br />
<br />
#####################################################<br />
# COLORING<br />
chemical_matching yes<br />
case_sensitive no<br />
match 1 1 <br />
match 2 2<br />
match 3 3<br />
match 4 4<br />
match 5 5<br />
match 6 6<br />
match 7 7<br />
match 1 8<br />
match 2 8<br />
match 3 8<br />
match 4 8<br />
match 5 8<br />
match 6 8<br />
match 1 9<br />
match 4 9<br />
match 2 10<br />
match 3 10<br />
match 7 11<br />
match 3 11<br />
match 4 11<br />
match 3 12<br />
match 4 12<br />
match 1 13<br />
match 3 13<br />
match 2 14<br />
match 4 14<br />
match 2 15<br />
match 3 15<br />
match 4 15<br />
match 1 16<br />
match 3 16<br />
match 4 16<br />
#####################################################<br />
Make sure you point to the colored matching spheres<br />
##################################################### <br />
## INPUT FILES / THINGS THAT CHANGE<br />
receptor_sphere_file ../dockfiles/matching_spheres.cl.sph</div>Jklyu