http://wiki.docking.org/api.php?action=feedcontributions&feedformat=atom&user=MkorczDISI - User contributions [en]2026-04-05T20:36:14ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Preparing_the_ligand&diff=5334Preparing the ligand2013-01-17T00:26:02Z<p>Mkorcz: </p>
<hr />
<div>=Preparing a ligand=<br />
<br />
==Automatic way, starting from SMILES==<br />
<br />
This way, you will make use of John's automatic scripts for database<br />
preparation and actually upload new molecules to a special section of<br />
[http://zinc.docking.org/ ZINC].<br />
<br />
*it is advisable to create a special subdirectory, since many new files will be generated. <br />
*the file containing the [http://www.daylight.com/smiles/ SMILES] strings should contain a string followed by an identifier on each line. <br />
*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.<br />
*run <tt>dbgen.csh yourname.smi</tt>. <br />
** Note that the dbgen.csh does not work for more that 1000 molecules.<br />
** Brake up your molecules into chunks of 1000 and run dbgen on each chunk.<br />
** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly. <br />
*you should obtain a file <tt>somename.db.gz</tt> .<br />
<br />
===optional===<br />
To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.<br />
*At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.<br />
***SetMaxConfs(600) #set to higher numbers ie. 1000<br />
***SetRMSThreshold(0.80) #set to lower numbers ie. 0.50<br />
***SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules<br />
*WARNING this should only be done if generating conformations for a small set of compounds!!!<br />
<br />
==Manual way==<br />
<br />
===Isolating the ligand as <tt>.mol2</tt> file===<br />
<br />
*extract the ligand structure from the <tt>.pdb</tt> file. <br />
*assign hydrogens. <br />
*assign all atom ([http://www.tripos.com/mol2/atom_types.html Sybyl/TAFF]) and bond types. <br />
*save it as <tt>ligandname.mol2</tt> file. <br />
<br />
===Running <tt>omega</tt> ===<br />
<br />
*run [http://www.eyesopen.com/products/applications/omega.html OMEGA], but don't ask me how to do that yet.<br />
<br />
===Running amsol===<br />
<br />
*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage]. <br />
*<tt>mkdir ./amsol2</tt> <br />
*Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!<br />
<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt> <br />
*edit <tt>./amsol2/someothername.mol2</tt> : <br />
*<br />
*delete all lines prior to <tt>@<TRIPOS>MOLECULE</tt> <br />
*<br />
*change line 2 (molecule name) to something of the format <tt>ABCD12345678</tt> (four capital letters followed by eight numbers). <br />
*<br />
*line 3 should be <tt>n<sub>atoms</sub> n<sub>bonds</sub> 0 0 0</tt><br />
*<br />
*the <tt>@<TRIPOS>MOLECULE</tt> section must consist of exactly '''5''' lines (adjust by adding/deleting blanks). <br />
*<br />
*remove all sections after the <tt>@<TRIPOS>BOND</tt> section.<br />
*<br />
*delete the blank lines between the <tt>ATOM</tt> and <tt>BOND</tt> sections, if there are any. <br />
*run <tt>RunAMSOL3.csh WAIT</tt> <br />
*the output <tt>someothername.solv</tt> file will contain the following:<br />
{| style="text-align: center; border:1px solid #aaa; margin: 1em 1em 1em 0; background: #f9f9f9; border-collapse: collapse;" cellpadding="5" cellspacing="0" <br />
|+ '''AMSOL output'''<br />
|-<br />
! style="border:1px #aaa solid; padding: 0.2em;" | line #1<br />
| style="border:1px #aaa solid; padding: 0.2em;" | molname || style="border:1px #aaa solid; padding: 0.2em;" | <math>n_{atoms}</math> || style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv<br />
|-<br />
! style="border:1px #aaa solid; padding: 0.2em;" | other lines <br />
| style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv<br />
|-<br />
| style="border:1px #aaa solid; padding: 0.2em;" | ''(per_atom)''<br />
|}<br />
<br />
<br />
*furthermore, there will be <tt>someothername.nmol2</tt> file which contains the correct partial charges.<br />
<br />
===Running <tt>mol2db</tt> ===<br />
<br />
*edit <tt>someothername.nmol2</tt> so that the <tt>@<TRIPOS>MOLECULE</tt> section consists of exactly '''6''' lines. <br />
*edit the <tt>inhier</tt> file so that the 'mol2_file', 'db_file' and 'solvation_table' entries are correct. <br />
*run <tt>mol2db inhier</tt> <br />
*add the preamble at the top of the file. <br />
*<tt>gzip</tt> the resulting file so that it can be used by <tt>DOCK</tt> .<br />
<br />
[[Category:Manual_DOCK]]<br />
[[Category:Tutorials]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Preparing_the_ligand&diff=5333Preparing the ligand2013-01-17T00:13:41Z<p>Mkorcz: </p>
<hr />
<div>=Preparing a ligand=<br />
<br />
==Automatic way, starting from SMILES==<br />
<br />
This way, you will make use of John's automatic scripts for database<br />
preparation and actually upload new molecules to a special section of<br />
[http://zinc.docking.org/ ZINC].<br />
<br />
*it is advisable to create a special subdirectory, since many new files will be generated. <br />
*the file containing the [http://www.daylight.com/smiles/ SMILES] strings should contain a string followed by an identifier on each line. <br />
*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.<br />
*run <tt>dbgen.csh yourname.smi</tt>. <br />
** Note that the dbgen.csh does not work for more that 1000 molecules.<br />
** Brake up your molecules into chunks of 1000 and run dbgen on each chunk.<br />
** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly. <br />
*you should obtain a file <tt>somename.db.gz</tt> .<br />
===<br />
WARNING this should only be done if generating conformations for a very small set of compounds!!!<br />
To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.<br />
*At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.<br />
SetMaxConfs(600) #set to higher numbers ie. 1000<br />
SetRMSThreshold(0.80) #set to lower numbers ie. 0.50<br />
SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules<br />
<br />
<br />
==Manual way==<br />
<br />
===Isolating the ligand as <tt>.mol2</tt> file===<br />
<br />
*extract the ligand structure from the <tt>.pdb</tt> file. <br />
*assign hydrogens. <br />
*assign all atom ([http://www.tripos.com/mol2/atom_types.html Sybyl/TAFF]) and bond types. <br />
*save it as <tt>ligandname.mol2</tt> file. <br />
<br />
===Running <tt>omega</tt> ===<br />
<br />
*run [http://www.eyesopen.com/products/applications/omega.html OMEGA], but don't ask me how to do that yet.<br />
<br />
===Running amsol===<br />
<br />
*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage]. <br />
*<tt>mkdir ./amsol2</tt> <br />
*Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!<br />
<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt> <br />
*edit <tt>./amsol2/someothername.mol2</tt> : <br />
*<br />
*delete all lines prior to <tt>@<TRIPOS>MOLECULE</tt> <br />
*<br />
*change line 2 (molecule name) to something of the format <tt>ABCD12345678</tt> (four capital letters followed by eight numbers). <br />
*<br />
*line 3 should be <tt>n<sub>atoms</sub> n<sub>bonds</sub> 0 0 0</tt><br />
*<br />
*the <tt>@<TRIPOS>MOLECULE</tt> section must consist of exactly '''5''' lines (adjust by adding/deleting blanks). <br />
*<br />
*remove all sections after the <tt>@<TRIPOS>BOND</tt> section.<br />
*<br />
*delete the blank lines between the <tt>ATOM</tt> and <tt>BOND</tt> sections, if there are any. <br />
*run <tt>RunAMSOL3.csh WAIT</tt> <br />
*the output <tt>someothername.solv</tt> file will contain the following:<br />
{| style="text-align: center; border:1px solid #aaa; margin: 1em 1em 1em 0; background: #f9f9f9; border-collapse: collapse;" cellpadding="5" cellspacing="0" <br />
|+ '''AMSOL output'''<br />
|-<br />
! style="border:1px #aaa solid; padding: 0.2em;" | line #1<br />
| style="border:1px #aaa solid; padding: 0.2em;" | molname || style="border:1px #aaa solid; padding: 0.2em;" | <math>n_{atoms}</math> || style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv<br />
|-<br />
! style="border:1px #aaa solid; padding: 0.2em;" | other lines <br />
| style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv<br />
|-<br />
| style="border:1px #aaa solid; padding: 0.2em;" | ''(per_atom)''<br />
|}<br />
<br />
<br />
*furthermore, there will be <tt>someothername.nmol2</tt> file which contains the correct partial charges.<br />
<br />
===Running <tt>mol2db</tt> ===<br />
<br />
*edit <tt>someothername.nmol2</tt> so that the <tt>@<TRIPOS>MOLECULE</tt> section consists of exactly '''6''' lines. <br />
*edit the <tt>inhier</tt> file so that the 'mol2_file', 'db_file' and 'solvation_table' entries are correct. <br />
*run <tt>mol2db inhier</tt> <br />
*add the preamble at the top of the file. <br />
*<tt>gzip</tt> the resulting file so that it can be used by <tt>DOCK</tt> .<br />
<br />
[[Category:Manual_DOCK]]<br />
[[Category:Tutorials]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Preparing_the_ligand&diff=5332Preparing the ligand2013-01-17T00:13:12Z<p>Mkorcz: </p>
<hr />
<div>=Preparing a ligand=<br />
<br />
==Automatic way, starting from SMILES==<br />
<br />
This way, you will make use of John's automatic scripts for database<br />
preparation and actually upload new molecules to a special section of<br />
[http://zinc.docking.org/ ZINC].<br />
<br />
*it is advisable to create a special subdirectory, since many new files will be generated. <br />
*the file containing the [http://www.daylight.com/smiles/ SMILES] strings should contain a string followed by an identifier on each line. <br />
*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.<br />
*run <tt>dbgen.csh yourname.smi</tt>. <br />
** Note that the dbgen.csh does not work for more that 1000 molecules.<br />
** Brake up your molecules into chunks of 1000 and run dbgen on each chunk.<br />
** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly. <br />
*you should obtain a file <tt>somename.db.gz</tt> .<br />
<br />
WARNING this should only be done if generating conformations for a very small set of compounds!!!<br />
To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.<br />
*At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.<br />
SetMaxConfs(600) #set to higher numbers ie. 1000<br />
SetRMSThreshold(0.80) #set to lower numbers ie. 0.50<br />
SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules<br />
<br />
<br />
==Manual way==<br />
<br />
===Isolating the ligand as <tt>.mol2</tt> file===<br />
<br />
*extract the ligand structure from the <tt>.pdb</tt> file. <br />
*assign hydrogens. <br />
*assign all atom ([http://www.tripos.com/mol2/atom_types.html Sybyl/TAFF]) and bond types. <br />
*save it as <tt>ligandname.mol2</tt> file. <br />
<br />
===Running <tt>omega</tt> ===<br />
<br />
*run [http://www.eyesopen.com/products/applications/omega.html OMEGA], but don't ask me how to do that yet.<br />
<br />
===Running amsol===<br />
<br />
*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage]. <br />
*<tt>mkdir ./amsol2</tt> <br />
*Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!<br />
<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt> <br />
*edit <tt>./amsol2/someothername.mol2</tt> : <br />
*<br />
*delete all lines prior to <tt>@<TRIPOS>MOLECULE</tt> <br />
*<br />
*change line 2 (molecule name) to something of the format <tt>ABCD12345678</tt> (four capital letters followed by eight numbers). <br />
*<br />
*line 3 should be <tt>n<sub>atoms</sub> n<sub>bonds</sub> 0 0 0</tt><br />
*<br />
*the <tt>@<TRIPOS>MOLECULE</tt> section must consist of exactly '''5''' lines (adjust by adding/deleting blanks). <br />
*<br />
*remove all sections after the <tt>@<TRIPOS>BOND</tt> section.<br />
*<br />
*delete the blank lines between the <tt>ATOM</tt> and <tt>BOND</tt> sections, if there are any. <br />
*run <tt>RunAMSOL3.csh WAIT</tt> <br />
*the output <tt>someothername.solv</tt> file will contain the following:<br />
{| style="text-align: center; border:1px solid #aaa; margin: 1em 1em 1em 0; background: #f9f9f9; border-collapse: collapse;" cellpadding="5" cellspacing="0" <br />
|+ '''AMSOL output'''<br />
|-<br />
! style="border:1px #aaa solid; padding: 0.2em;" | line #1<br />
| style="border:1px #aaa solid; padding: 0.2em;" | molname || style="border:1px #aaa solid; padding: 0.2em;" | <math>n_{atoms}</math> || style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv<br />
|-<br />
! style="border:1px #aaa solid; padding: 0.2em;" | other lines <br />
| style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv<br />
|-<br />
| style="border:1px #aaa solid; padding: 0.2em;" | ''(per_atom)''<br />
|}<br />
<br />
<br />
*furthermore, there will be <tt>someothername.nmol2</tt> file which contains the correct partial charges.<br />
<br />
===Running <tt>mol2db</tt> ===<br />
<br />
*edit <tt>someothername.nmol2</tt> so that the <tt>@<TRIPOS>MOLECULE</tt> section consists of exactly '''6''' lines. <br />
*edit the <tt>inhier</tt> file so that the 'mol2_file', 'db_file' and 'solvation_table' entries are correct. <br />
*run <tt>mol2db inhier</tt> <br />
*add the preamble at the top of the file. <br />
*<tt>gzip</tt> the resulting file so that it can be used by <tt>DOCK</tt> .<br />
<br />
[[Category:Manual_DOCK]]<br />
[[Category:Tutorials]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Dock_Ligand_Clustering&diff=1382Dock Ligand Clustering2012-02-08T19:59:14Z<p>Mkorcz: </p>
<hr />
<div>DOCK 3.6 Ligand Clustering<br />
<br />
* branch of [[DOCK_3.6]]<br />
* Contributed by Niu Huang's lab<br />
* Currently in the niu-nibs-clustering branch, ready for use<br />
* Replacement for single mode<br />
* Example INDOCK file parameters, add to your current INDOCK file<br />
<br />
#<br />
################################################################################<br />
# POSE_CLUSTERING<br />
#<br />
pose_clustering yes<br />
# "yes/no" General switch of pose clustering (default: no)<br />
pose_clustering_detail no<br />
# "yes/no" Switch of print out detail infomation (default: no)<br />
pose_clustering_method 0<br />
# 0---------Write all the poses<br />
# 1---------Clustering method based on KGS penalty function<br />
# 2---------Clustering method based on ratio of RANK and RMSD<br />
pose_clustering_cutoff 1.1<br />
# pre-determined variable for clustering cutoff<br />
# In method 0, the cutoff is unused.<br />
# In method 1, the cutoff is unused.<br />
# In method 2, the cutoff is Nc.<br />
################################################################################<br />
# cutoff in pose_clustering for saving resource<br />
#pose_clustering_RMSD_cutoff<br />
#pose_clustering_energy_cutoff no<br />
pose_clus_inputno_cutoff 0<br />
# number: input number cutoff; 0: no; -1: rotatable bond based (NA)<br />
# number of poses to be clustered according to energy rank<br />
# for method 0, it is also used.<br />
pose_clus_outputno_cutoff 0<br />
# number: output number cutoff; 0: no<br />
# number of clustered poses being written out according to energy rank<br />
# for method 0, it is also used.<br />
################################################################################<br />
<br />
Currently installed in<br />
<br />
~xyz/dockenv/bin/Linux/ligandclustering/<br />
<br />
Bonus: A version compiled with nsize=193 for use with Qnifft [[Qnifft_DOCK_3.6_conversion]] is in <br />
<br />
~xyz/dockenv/bin/Linux/ligandclustering-qnifft/<br />
<br />
Or where ~xyz/dockenv is your $DOCK_BASE<br />
<br />
[[Category:DOCK]]<br />
<br />
-----<br />
<br />
Currently (Feb 2012) if you have problems running the above script you may need a distmap file in your grids directory (just type 'distmap' in the grids directory and it should be created automatically, this will not be used in the calculations but it is something that dock needs to read in at this time) also add the line into INDOCK<br />
<br />
###############################################################################<br />
# SCORING<br />
#<br />
distmap_file ../grids/distmap<br />
<br />
You may also need to comment the random seed line out of the INDOCK file<br />
<br />
###############################################################################<br />
################## DOCK 3.5 INPUT PARAMETERS 2011/10/26 #######################<br />
###############################################################################<br />
###############################################################################<br />
# INPUT/OUTPUT<br />
#<br />
#random_seed 777</div>Mkorczhttp://wiki.docking.org/index.php?title=Scoreopt&diff=4325Scoreopt2012-02-08T19:46:46Z<p>Mkorcz: </p>
<hr />
<div>==Overview==<br />
<br />
Scoreopt allows you to rescore poses after a docking run is complete<br />
<br />
==Usage==<br />
<br />
Before using scoreopt, you should have a pdb (or eel1 or mol2) file with the poses to be rescored.<br />
<br />
$mud/doscoreopt.csh <filename.eel1> <path to grids><br />
<br />
<br />
Output is combine.rescores ( in the form of combine.scores ) <br />
<br />
<id> <shape> <elect> <VdW> <polar solv> <apolar solv> <total> <subdir><br />
<br />
<br />
==If You Have Problems==<br />
<br />
If you do not have an eel1 file or things are not running smoothly with your pdb file here are two options of how to get around it.<br />
<br />
An eel1 file can be automatically created for you with this script:<br />
<br />
$mud/to_eel1.csh your.pdb (see http://wiki.bkslab.org/index.php/Analysing_the_results for further directions)<br />
<br />
If you have special molecules the other way to approch this problem is to:<br />
<br />
a) read your pdb into chimera<br />
<br />
b) add hydrogens in chimera ('Tools_>Structure Editing->AddH' show labels at that time 'Actions->Lable->IDATM type' and make sure you are happy with the molecule) <br />
<br />
c) charge the molecule in chimera ('Tools->Structure Editing-> AddCharge')<br />
<br />
d) write out the molecule out as a filename.mol2 <br />
<br />
e) run the scoreopt script from above<br />
<br />
----- <br />
<br />
If things are still not working just see the header of the .mol2 file and make sure that the header is in the correct format (there should only be 5 lines between @<TRIPOS>MOLECULE and @<TRIPOS>ATOM, and the new to_eel1.mol2 created in line two should have a new label in the format of four letters and eight numbers ie. AAAA12345678.)<br />
<br />
WRONG Header !!!!!<br />
----------------<br />
@<TRIPOS>MOLECULE<br />
<br />
obj16.pdb<br />
<br />
15 15 1 0 0<br />
<br />
SMALL<br />
<br />
NO_CHARGES<br />
<br />
<br />
<br />
@<TRIPOS>ATOM<br />
----------------<br />
<br />
RIGHT Header !!!!<br />
----------------<br />
@<TRIPOS>MOLECULE<br />
<br />
TEMP12345678<br />
<br />
24 24 0 0 0<br />
<br />
SMALL<br />
<br />
USER_CHARGES<br />
<br />
<br />
@<TRIPOS>ATOM<br />
----------------</div>Mkorczhttp://wiki.docking.org/index.php?title=Scoreopt&diff=4324Scoreopt2012-02-08T19:29:04Z<p>Mkorcz: </p>
<hr />
<div>==Overview==<br />
<br />
Scoreopt allows you to rescore poses after a docking run is complete<br />
<br />
==Usage==<br />
<br />
Before using scoreopt, you should have a pdb (or eel1 or mol2) file with the poses to be rescored.<br />
<br />
$mud/doscoreopt.csh <filename.eel1> <path to grids><br />
<br />
<br />
Output is combine.rescores ( in the form of combine.scores ) <br />
<br />
<id> <shape> <elect> <VdW> <polar solv> <apolar solv> <total> <subdir><br />
<br />
<br />
------<br />
If you do not have an eel1 file and things are not running smoothly with your pdb file here are two options of how to get around it.<br />
<br />
An eel1 file can be automatically created for you with this script:<br />
<br />
$mud/to_eel1.csh your.pdb (see http://wiki.bkslab.org/index.php/Analysing_the_results for further directions)<br />
<br />
If you have special molecules the other was around it is to:<br />
a) read your pdb into chimera<br />
b) add hydrogens in chimera ('Tools_>Structure Editing->AddH' show labels at that time 'Actions->Lable->IDATM type' and make sure you are happy with the molecule) <br />
c) charge the molecule in chimera ('Tools->Structure Editing-> AddCharge')<br />
d) write out the molecule out as a filename.mol2 <br />
d) run the scoreopt script from above</div>Mkorczhttp://wiki.docking.org/index.php?title=Pka&diff=3931Pka2011-09-15T17:35:05Z<p>Mkorcz: </p>
<hr />
<div>'''Experimental''' pKa values<br />
<br />
Please add any useful lists of experimentally determined pKa values you know of to the list:<br />
<br />
http://www.chem.wisc.edu/areas/reich/pkatable/index.htm[http://www.chem.wisc.edu/areas/reich/pkatable/index.htm]<br />
<br />
http://pubs.acs.org/doi/suppl/10.1021/ci100019p[http://pubs.acs.org/doi/suppl/10.1021/ci100019p]<br />
<br />
http://evans.harvard.edu/pdf/evans_pKa_table.pdf[http://evans.harvard.edu/pdf/evans_pKa_table.pdf]<br />
<br />
'''Computational''' pKa programs<br />
<br />
http://ibmlc2.chem.uga.edu/sparc/index.cfm[http://ibmlc2.chem.uga.edu/sparc/index.cfm] - can do multiple things, so you have to select the "pKa" button first, then draw molecule/insert smiles, and finally press "calculate". Has also a database of known values ("Search DB"). <br />
<br />
ChemAxon's[http://www.chemaxon.com/] Marvin/Calculator plugins has a pKa calculation option that looks quite elaborate. You can can try it online. Can't say how good it it is yet. Academics can apply for a free academic license. Lab copy is in /raid3/software/jchem/current/bin/mview. You have to cd to that directory then run it.<br />
<br />
It is now included in the new dockenv, therefore you can just type mview in your terminal. <br />
<br />
Add your favorites.</div>Mkorczhttp://wiki.docking.org/index.php?title=Pka&diff=3930Pka2011-09-15T17:34:46Z<p>Mkorcz: </p>
<hr />
<div>'''Experimental''' pKa values<br />
<br />
Please add any useful lists of experimentally determined pKa values you know of to the list:<br />
<br />
http://www.chem.wisc.edu/areas/reich/pkatable/index.htm[http://www.chem.wisc.edu/areas/reich/pkatable/index.htm]<br />
<br />
http://pubs.acs.org/doi/suppl/10.1021/ci100019p[http://pubs.acs.org/doi/suppl/10.1021/ci100019p]<br />
<br />
http://evans.harvard.edu/pdf/evans_pKa_table.pdf[http://evans.harvard.edu/pdf/evans_pKa_table.pdf]<br />
<br />
'''Computational''' pKa programs<br />
<br />
http://ibmlc2.chem.uga.edu/sparc/index.cfm[http://ibmlc2.chem.uga.edu/sparc/index.cfm] - can do multiple things, so you have to select the "pKa" button first, then draw molecule/insert smiles, and finally press "calculate". Has also a database of known values ("Search DB"). <br />
<br />
ChemAxon's[http://www.chemaxon.com/] Marvin/Calculator plugins has a pKa calculation option that looks quite elaborate. You can can try it online. Can't say how good it it is yet. Academics can apply for a free academic license. Lab copy is in /raid3/software/jchem/current/bin/mview. You have to cd to that directory then run it.<br />
<br />
It is also now included in the new dockenv, therefore you can just type mview in your terminal. <br />
<br />
Add your favorites.</div>Mkorczhttp://wiki.docking.org/index.php?title=INDOCK_for_DOCK_3.6&diff=3352INDOCK for DOCK 3.62011-09-13T23:49:53Z<p>Mkorcz: </p>
<hr />
<div>What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are comments.<br />
<br />
Required first line:<br />
<br />
DOCK 3.5 parameter<br />
###############################################################################<br />
################## DOCK 3.5 INPUT PARAMETERS 2011/09/07 #######################<br />
###############################################################################<br />
###############################################################################<br />
# INPUT/OUTPUT<br />
#<br />
<br />
This is the path to the receptor matching spheres file. Most scripts make a set of directories and copy the INDOCK file into them, so this path sometimes has an extra set of "../" in it compared to what you might think. If you use [[DOCK Blaster]]. Generally, match3 has more spheres than match2, so produces more possible orientations. These spheres are matched to ligand spheres, generated from heavy atoms in the "rigid component" of each ligand. For more about the rigid component, see [[Flexibase Format]].<br />
<br />
receptor_sphere_file ../../sph/match3.sph<br />
<br />
The next line is always 1, and is marked for deprecation.<br />
<br />
cluster_numbers 1<br />
<br />
The next line refers to which ligand file to use. If using many of the automated scripts, split_database_index is used, as this allows many ligand files (or just 1) to be placed in the split_database_index file and read in one after another during a DOCK run. If docking small things on your own, you can change this to any file.<br />
<br />
# NOTE: split_database_index is reserved to specify a list of files<br />
ligand_atom_file split_database_index<br />
<br />
This will control the file output, again many of the automated scripts expect it to be test. OUTDOCK files are always named OUTDOCK.<br />
<br />
output_file_prefix test.<br />
<br />
This controls the random seed used in the minimization procedure. Changing this will produce slightly different results.<br />
<br />
random_seed 777<br />
#<br />
###############################################################################<br />
# MATCHING<br />
#<br />
<br />
distance_tolerance is how different the distances can be between a pair of receptor matching spheres and a pair of ligand matching spheres for them to still be considered matched.<br />
<br />
distance_tolerance 1.5<br />
<br />
This changes how many spheres must be matched to generate an orientation. 3 as a minimum, 4 as a maximum is generally accepted as the right thing to use. Less than 3 is too degenerate to generate an actual orientation, and requiring more than 4 matched spheres does not work well, since we only use heavy atoms in ring systems to generate ligand matching spheres.<br />
<br />
nodes_maximum 4<br />
nodes_minimum 3<br />
<br />
The next 4 parameters control how the histograms of distance differences are generated. The binsize is how big the bins are, the overlap controls if a sphere can be put into multiple bins. The ligand & receptor parameters are not required to be the same. <br />
<br />
ligand_binsize 0.4<br />
ligand_overlap 0.2<br />
receptor_binsize 0.4<br />
receptor_overlap 0.2<br />
<br />
Bumping is using a quick check of distances when placing ligand atoms in the binding site to determine if they have a steric clash. The maximum is how many can be 'bumped' or in close steric contact per rigid or flexible component of the ligand, as per the [[Flexibase Format]]. Even ligands with some steric clashes can sometimes be rescued by minimization. Setting this number very high will cause many clashed orientations to be scored, which can be prohibitively slow.<br />
<br />
bump_maximum 1<br />
<br />
The next four parameters are unused and unsupported.<br />
<br />
focus_cycles 0<br />
focus_bump 0 <br />
focus_type energy<br />
critical_clusters no<br />
#<br />
###############################################################################<br />
# COLORING<br />
#<br />
<br />
This controls whether chemical matching or coloring is used at all. If yes, many match lines are necessary. These may not be perfect, but [[DOCK Blaster]] has been using these for a long time. Setting this to no produces many more matched orientations, which can be slow, but can help you understand exactly what the energy function is doing.<br />
<br />
chemical_matching yes<br />
case_sensitive no<br />
# ligand color, receptor color<br />
match positive negative<br />
match positive negative_or_acceptor<br />
match positive not_neutral<br />
match negative positive<br />
match negative positive_or_donor<br />
match negative not_neutral<br />
match donor acceptor<br />
match donor donacc<br />
match donor negative_or_acceptor<br />
match donor neutral_or_acceptor_or_donor<br />
match donor not_neutral<br />
match acceptor donor<br />
match acceptor donacc<br />
match acceptor positive_or_donor<br />
match acceptor neutral_or_acceptor_or_donor<br />
match acceptor not_neutral<br />
match neutral neutral<br />
match neutral neutral_or_acceptor_or_donor<br />
match ester_o donor<br />
match ester_o donacc<br />
match ester_o positive_or_donor<br />
match ester_o not_neutral<br />
match amide_o donor<br />
match amide_o donacc<br />
match amide_o positive_or_donor<br />
match amide_o not_neutral<br />
<br />
Single mode is deprecated, these parameters won't work. See [[Dock Ligand Clustering]]<br />
#<br />
###############################################################################<br />
# SINGLE MODE<br />
#<br />
#rmsd_override 0.0<br />
#contact_minimum 0<br />
#energy_maximum 1.0e+6<br />
##truncate_output 1000.0<br />
#<br />
<br />
Search mode is now the default/only mode of docking. Each parameter is described below.<br />
<br />
###############################################################################<br />
# SEARCH MODE<br />
#<br />
<br />
The ratio_minimum parameter has been slated for deprecation.<br />
<br />
ratio_minimum 0.0<br />
<br />
These parameters control how many atoms are necessary in the ligand for it to be docked.<br />
<br />
atom_minimum 5 <br />
atom_maximum 100<br />
<br />
How many of the top molecules will be saved in the output test.* file. <br />
<br />
number_save 50000<br />
<br />
The maximum number of molecules that will be scored in any given run.<br />
<br />
molecules_maximum 300000 <br />
<br />
How many molecules will be skipped, this feature currently does not work.<br />
<br />
initial_skip 0<br />
<br />
How long a molecule is processed before quitting. This feature currently may not work as expected.<br />
<br />
timeout 180<br />
<br />
There are many scoring options:<br />
<br />
# <br />
###############################################################################<br />
# SCORING<br />
#<br />
<br />
Valid options for ligand_desolvation are 'volume' (partial desolvation a la Mysinger & Shoichet 2010), 'full' meaning that the entire ligand is assumed to be desolvated in the binding site and 'none', where no desolvation penalties are applied.<br />
<br />
ligand_desolvation volume<br />
<br />
See the note about relative paths for the matching spheres above, the same comments apply here. There are 2 ways to run 'volume' or partial desolvation, one is to use one grid for every ligand atom like this:<br />
<br />
solvmap_file ../../grids/solvmap_sev<br />
<br />
The other option is to use one grid for ligand heavy atoms and one for ligand hydrogen atoms, you'll want to uncomment these lines to use them (and comment out the other solvmap_file line).<br />
<br />
#solvmap_file ../../grids/solvmap_sev.heavy<br />
#hydrogen_solvmap_file ../../grids/solvmap.sev.hydrogen<br />
<br />
This is the phimap file used for electrostatic scoring. For a better understanding of this grid, see [[Visualizing delphi]].<br />
<br />
delphi_file ../../grids/rec+sph.phi<br />
<br />
This controls the chemgrid file, which contains the van der Waals scoring for every coordinate (chem.vdw will be called) as well as the distance map grids that will be used for deciphering bumping (chem.bmp will be called).<br />
<br />
chemgrid_file_prefix ../../grids/chem<br />
<br />
This is the parameter file that contains the atom type definitions:<br />
<br />
vdw_parameter_file ../../grids/vdw.parms.amb.mindock<br />
<br />
The following options allow the electrostatics and van der Waals parameters to be scaled relative to each other and the solvation scoring.<br />
<br />
electrostatic_scale 1.0<br />
vdw_scale 1.0<br />
<br />
The following parameter lets ligands with internal steric clashes attempt to find a ligand conformation that scores well but does not have any internal clashes. Sometimes this procedure will fail in circumstances where there are many flexible branches, or where a ligand that is too large for the binding site is being docked.<br />
<br />
check_clashes yes<br />
<br />
If set to yes, this removes the positive solvation from each ligand atom and spreads it evenly over the molecule. This is not suggested.<br />
<br />
remove_positive_solvation no<br />
<br />
After each orientation of the rigid component is processed and the many ligand conformations have been examined, the best ligand conformation for that orientation can be minimized using the following parameters.<br />
<br />
#<br />
###############################################################################<br />
# MINIMIZATION<br />
#<br />
<br />
No turns off minimization completely.<br />
<br />
minimize yes<br />
<br />
Don't minimize molecules that score above the minimization_max.<br />
<br />
minimization_max 1.0e15<br />
<br />
If set to yes, this checks to see if the orientation has already been scored and quits. This has not been tested recently.<br />
<br />
check_degeneracy no<br />
<br />
How many iterations of minimization to do. More means longer run times, but potentially better poses.<br />
<br />
simplex_iterations 250<br />
<br />
How much the total energy can changed to be considered converged. Setting this higher will stop faster, setting it lower will cause it to do more iterations before converging (or potentially hitting the iteration max above).<br />
<br />
simplex_convergence 0.1<br />
<br />
If the energy changes by this much, restart the minimizer from this newest position.<br />
<br />
simplex_restart 1.0<br />
<br />
This is the initial distance in angstroms the molecule is translated (note that translation and rotation used to be swapped for many releases of DOCK).<br />
<br />
simplex_initial_translation 0.2<br />
<br />
How many degrees of initial rotation are done.<br />
<br />
simplex_initial_rotation 5.0<br />
#<br />
###############################################################################<br />
###############################################################################</div>Mkorczhttp://wiki.docking.org/index.php?title=INDOCK_for_DOCK_3.6&diff=3351INDOCK for DOCK 3.62011-09-13T23:48:24Z<p>Mkorcz: </p>
<hr />
<div>What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are comments.<br />
<br />
Required first line:<br />
<br />
DOCK 3.5 parameter<br />
###############################################################################<br />
################## DOCK 3.5 INPUT PARAMETERS 2011/09/07 #######################<br />
###############################################################################<br />
###############################################################################<br />
# INPUT/OUTPUT<br />
#<br />
<br />
This is the path to the receptor matching spheres file. Most scripts make a set of directories and copy the INDOCK file into them, so this path sometimes has an extra set of "../" in it compared to what you might think. If you use [[DOCK Blaster]]. Generally, match3 has more spheres than match2, so produces more possible orientations. These spheres are matched to ligand spheres, generated from heavy atoms in the "rigid component" of each ligand. For more about the rigid component, see [[Flexibase Format]].<br />
<br />
receptor_sphere_file ../../sph/match3.sph<br />
<br />
The next line is always 1, and is marked for deprecation.<br />
<br />
cluster_numbers 1<br />
<br />
The next line refers to which ligand file to use. If using many of the automated scripts, split_database_index is used, as this allows many ligand files (or just 1) to be placed in the split_database_index file and read in one after another during a DOCK run. If docking small things on your own, you can change this to any file.<br />
<br />
# NOTE: split_database_index is reserved to specify a list of files<br />
ligand_atom_file split_database_index<br />
<br />
This will control the file output, again many of the automated scripts expect it to be test. OUTDOCK files are always named OUTDOCK.<br />
<br />
output_file_prefix test.<br />
<br />
This controls the random seed used in the minimization procedure. Changing this will produce slightly different results.<br />
<br />
random_seed 777<br />
#<br />
###############################################################################<br />
# MATCHING<br />
#<br />
<br />
distance_tolerance is how different the distances can be between a pair of receptor matching spheres and a pair of ligand matching spheres for them to still be considered matched.<br />
<br />
distance_tolerance 1.5<br />
<br />
This changes how many spheres must be matched to generate an orientation. 3 as a minimum, 4 as a maximum is generally accepted as the right thing to use. Less than 3 is too degenerate to generate an actual orientation, and requiring more than 4 matched spheres does not work well, since we only use heavy atoms in ring systems to generate ligand matching spheres.<br />
<br />
nodes_maximum 4<br />
nodes_minimum 3<br />
<br />
The next 4 parameters control how the histograms of distance differences are generated. The binsize is how big the bins are, the overlap controls if a sphere can be put into multiple bins. The ligand & receptor parameters are not required to be the same. <br />
<br />
ligand_binsize 0.4<br />
ligand_overlap 0.2<br />
receptor_binsize 0.4<br />
receptor_overlap 0.2<br />
<br />
Bumping is using a quick check of distances when placing ligand atoms in the binding site to determine if they have a steric clash. The maximum is how many can be 'bumped' or in close steric contact per rigid or flexible component of the ligand, as per the [[Flexibase Format]]. Even ligands with some steric clashes can sometimes be rescued by minimization. Setting this number very high will cause many clashed orientations to be scored, which can be prohibitively slow.<br />
<br />
bump_maximum 1<br />
<br />
The next four parameters are unused and unsupported.<br />
<br />
focus_cycles 0<br />
focus_bump 0 <br />
focus_type energy<br />
critical_clusters no<br />
#<br />
###############################################################################<br />
# COLORING<br />
#<br />
<br />
This controls whether chemical matching or coloring is used at all. If yes, many match lines are necessary. These may not be perfect, but [[DOCK Blaster]] has been using these for a long time. Setting this to no produces many more matched orientations, which can be slow, but can help you understand exactly what the energy function is doing.<br />
<br />
chemical_matching yes<br />
case_sensitive no<br />
# ligand color, receptor color<br />
match positive negative<br />
match positive negative_or_acceptor<br />
match positive not_neutral<br />
match negative positive<br />
match negative positive_or_donor<br />
match negative not_neutral<br />
match donor acceptor<br />
match donor donacc<br />
match donor negative_or_acceptor<br />
match donor neutral_or_acceptor_or_donor<br />
match donor not_neutral<br />
match acceptor donor<br />
match acceptor donacc<br />
match acceptor positive_or_donor<br />
match acceptor neutral_or_acceptor_or_donor<br />
match acceptor not_neutral<br />
match neutral neutral<br />
match neutral neutral_or_acceptor_or_donor<br />
match ester_o donor<br />
match ester_o donacc<br />
match ester_o positive_or_donor<br />
match ester_o not_neutral<br />
match amide_o donor<br />
match amide_o donacc<br />
match amide_o positive_or_donor<br />
match amide_o not_neutral<br />
<br />
Single mode is deprecated, these parameters won't work. See [[Dock Ligand Clustering]]<br />
#<br />
###############################################################################<br />
# SINGLE MODE<br />
#<br />
#rmsd_override 0.0<br />
#contact_minimum 0<br />
#energy_maximum 1.0e+6<br />
##truncate_output 1000.0<br />
#<br />
<br />
Search mode is now the default/only mode of docking. Each parameter is described below.<br />
<br />
###############################################################################<br />
# SEARCH MODE<br />
#<br />
<br />
The ratio_minimum parameter has been slated for deprecation.<br />
<br />
ratio_minimum 0.0<br />
<br />
These parameters control how many atoms are necessary in the ligand for it to be docked.<br />
<br />
atom_minimum 5 <br />
atom_maximum 100<br />
<br />
How many of the top molecules will be saved in the output test.* file. <br />
<br />
number_save 50000<br />
<br />
The maximum number of molecules that will be scored in any given run.<br />
<br />
molecules_maximum 300000 <br />
<br />
How many molecules will be skipped, this feature currently does not work.<br />
<br />
initial_skip 0<br />
<br />
How long a molecule is processed before quitting. This feature currently may not work as expected.<br />
<br />
timeout 180<br />
<br />
There are many scoring options:<br />
<br />
# <br />
###############################################################################<br />
# SCORING<br />
#<br />
<br />
Valid options for ligand_desolvation are 'volume' (partial desolvation a la Mysinger & Shoichet 2010), 'full' meaning that the entire ligand is assumed to be desolvated in the binding site and 'none', where no desolvation penalties are applied.<br />
<br />
ligand_desolvation volume<br />
<br />
See the note about relative paths for the matching spheres above, the same comments apply here. There are 2 ways to run 'volume' or partial desolvation, one is to use one grid for every ligand atom like this:<br />
<br />
solvmap_file ../../grids/solvmap_sev<br />
<br />
The other option is to use one grid for ligand heavy atoms and one for ligand hydrogen atoms, you'll want to uncomment these lines to use them (and comment out the other solvmap_file line).<br />
<br />
#solvmap_file ../../grids/solvmap_sev.heavy<br />
#hydrogen_solvmap_file ../../grids/solvmap.sev.hydrogen<br />
<br />
This is the phimap file used for electrostatic scoring. For a better understanding of this grid, see [[Visualizing delphi]].<br />
<br />
delphi_file ../../grids/rec+sph.phi<br />
<br />
This controls the chemgrid file, which contains the van der Waals scoring for every coordinate (chem.vdw will be called) as well as the distance map grids that will be used for decipering bumping (chem.bmp will be called).<br />
<br />
chemgrid_file_prefix ../../grids/chem<br />
<br />
This is the parameter file that contains the atom type definitions:<br />
<br />
vdw_parameter_file ../../grids/vdw.parms.amb.mindock<br />
<br />
The following options allow the electrostatics and van der Waals parameters to be scaled relative to each other and the solvation scoring.<br />
<br />
electrostatic_scale 1.0<br />
vdw_scale 1.0<br />
<br />
The following parameter lets ligands with internal steric clashes attempt to find a ligand conformation that scores well but does not have any internal clashes. Sometimes this procedure will fail in circumstances where there are many flexible branches, or where a ligand that is too large for the binding site is being docked.<br />
<br />
check_clashes yes<br />
<br />
If set to yes, this removes the positive solvation from each ligand atom and spreads it evenly over the molecule. This is not suggested.<br />
<br />
remove_positive_solvation no<br />
<br />
After each orientation of the rigid component is processed and the many ligand conformations have been examined, the best ligand conformation for that orientation can be minimized using the following parameters.<br />
<br />
#<br />
###############################################################################<br />
# MINIMIZATION<br />
#<br />
<br />
No turns off minimization completely.<br />
<br />
minimize yes<br />
<br />
Don't minimize molecules that score above the minimization_max.<br />
<br />
minimization_max 1.0e15<br />
<br />
If set to yes, this checks to see if the orientation has already been scored and quits. This has not been tested recently.<br />
<br />
check_degeneracy no<br />
<br />
How many iterations of minimization to do. More means longer run times, but potentially better poses.<br />
<br />
simplex_iterations 250<br />
<br />
How much the total energy can changed to be considered converged. Setting this higher will stop faster, setting it lower will cause it to do more iterations before converging (or potentially hitting the iteration max above).<br />
<br />
simplex_convergence 0.1<br />
<br />
If the energy changes by this much, restart the minimizer from this newest position.<br />
<br />
simplex_restart 1.0<br />
<br />
This is the initial distance in angstroms the molecule is translated (note that translation and rotation used to be swapped for many releases of DOCK).<br />
<br />
simplex_initial_translation 0.2<br />
<br />
How many degrees of initial rotation are done.<br />
<br />
simplex_initial_rotation 5.0<br />
#<br />
###############################################################################<br />
###############################################################################</div>Mkorczhttp://wiki.docking.org/index.php?title=Decoys&diff=1322Decoys2011-09-08T22:42:06Z<p>Mkorcz: </p>
<hr />
<div>Decoys are...<br />
<br />
Decoys are important for judging the performance of [[molecular docking]] algorithms. <br />
<br />
The [[DUD database]] is a free directory of useful decoys for [[virtual screening]].<br />
<br />
For more information on preparation see<br />
<br />
[[Automated_Database_Preparation#Automatic_Decoy_Generation]]<br />
<br />
<br />
== People working on Decoys == <br />
<br />
* Alan<br />
* Michael<br />
<br />
<br />
[[Category:Concepts]]<br />
[[Category:DOCK:Scoring problem]]<br />
[[Category:DOCK:Sampling problem]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Decoys&diff=1321Decoys2011-09-08T22:41:40Z<p>Mkorcz: </p>
<hr />
<div>Decoys are...<br />
<br />
Decoys are important for judging the performance of [[molecular docking]] algorithms. <br />
<br />
The [[DUD database]] is a free directory of useful decoys for [[virtual screening]].<br />
<br />
For more information on preparation see<br />
<br />
[[Automated_Database_Preparation]]<br />
<br />
<br />
== People working on Decoys == <br />
<br />
* Alan<br />
* Michael<br />
<br />
<br />
[[Category:Concepts]]<br />
[[Category:DOCK:Scoring problem]]<br />
[[Category:DOCK:Sampling problem]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Pymol_background&diff=4196Pymol background2010-10-21T23:29:21Z<p>Mkorcz: </p>
<hr />
<div>There are two ways to set the PyMOL background to be transparent.<br />
<br />
1) Open PyMOL your usual way, then turn off the opaque background(default is on) by click in the menue bar on Display -> Background -> Opaque. Now you can ray trace and save your image as a png file.<br />
<br />
2) You may add the commad '''''set ray_opaque_background, off''''' to your script or on the command line.<br />
<br />
Enjoy!</div>Mkorczhttp://wiki.docking.org/index.php?title=Pymol_background&diff=4195Pymol background2010-10-21T23:27:58Z<p>Mkorcz: </p>
<hr />
<div></div>Mkorczhttp://wiki.docking.org/index.php?title=Pymol_background&diff=4194Pymol background2010-10-21T23:22:02Z<p>Mkorcz: </p>
<hr />
<div>There are two ways to set the PyMOL background to be transparent.<br />
<br />
1) Open PyMOL your usual way, then turn off the opaque background(default is on) by click in the menue bar on Display -> Background -> Opaque. Now you can ray trace and save your image as a .png.<br />
<br />
2) You may add the commad '''''set ray_opaque_background, off''''' to your script or on the command line.<br />
<br />
Enjoy!</div>Mkorczhttp://wiki.docking.org/index.php?title=Pymol_background&diff=4193Pymol background2010-10-21T23:21:49Z<p>Mkorcz: </p>
<hr />
<div>There are two ways to set the PyMOL background to be transparent.<br />
<br />
1) Open PyMOL your usual way, then turn off the opaque background(default is on) by click in the menue bar on Display -> Background -> Opaque. Now you can ray trace and save your image as a .png.<br />
<br />
2) You may add the commad '''''set ray_opaque_background, off''''' to your script or on the command line.<br />
<br />
Enjoy!</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4355Shoichet Lab Photos2010-10-20T07:22:39Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
<br />
February<br />
<br />
March<br />
<br />
April<br />
<br />
May<br />
<br />
June<br />
<br />
July<br />
<br />
August<br />
<br />
September<br />
<br />
October<br />
<br />
November<br />
<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:004.jpeg]][[Image:008.jpeg]]<br />
[[Image:007.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:014.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]][[Image:Twin03.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4354Shoichet Lab Photos2010-10-20T07:21:33Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
<br />
February<br />
<br />
March<br />
<br />
April<br />
<br />
May<br />
<br />
June<br />
<br />
July<br />
<br />
August<br />
<br />
September<br />
<br />
October<br />
<br />
November<br />
<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:004.jpeg]][[Image:008.jpeg]]<br />
[[Image:007.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]][[Image:Twin03.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4353Shoichet Lab Photos2010-10-20T07:20:40Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
<br />
February<br />
<br />
March<br />
<br />
April<br />
<br />
May<br />
<br />
June<br />
<br />
July<br />
<br />
August<br />
<br />
September<br />
<br />
October<br />
<br />
November<br />
<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:004.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]][[Image:Twin03.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4352Shoichet Lab Photos2010-10-20T07:18:27Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
<br />
February<br />
<br />
March<br />
<br />
April<br />
<br />
May<br />
<br />
June<br />
<br />
July<br />
<br />
August<br />
<br />
September<br />
<br />
October<br />
<br />
November<br />
<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]][[Image:Twin03.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4351Shoichet Lab Photos2010-10-20T07:16:44Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
<br />
February<br />
<br />
March<br />
<br />
April<br />
<br />
May<br />
<br />
June<br />
<br />
July<br />
<br />
August<br />
<br />
September<br />
<br />
October<br />
<br />
November<br />
<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]][[Image:Example.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4350Shoichet Lab Photos2010-10-20T05:48:01Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
<br />
February<br />
<br />
March<br />
<br />
April<br />
<br />
May<br />
<br />
June<br />
<br />
July<br />
<br />
August<br />
<br />
September<br />
<br />
October<br />
<br />
November<br />
<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4349Shoichet Lab Photos2010-10-20T05:47:26Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
February<br />
March<br />
April<br />
May<br />
June<br />
July<br />
August<br />
September<br />
October<br />
November<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4348Shoichet Lab Photos2010-10-20T05:45:53Z<p>Mkorcz: </p>
<hr />
<div>== '''2010''' ==<br />
January<br />
February <br />
March <br />
April <br />
May <br />
June<br />
July <br />
August<br />
September<br />
October<br />
November<br />
December<br />
<br />
'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4347Shoichet Lab Photos2010-10-13T19:34:27Z<p>Mkorcz: </p>
<hr />
<div>'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4346Shoichet Lab Photos2010-10-13T19:34:11Z<p>Mkorcz: </p>
<hr />
<div>'''Fun in the snow'''. Lab trip to lake Tahoe.<br />
[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4345Shoichet Lab Photos2010-10-13T19:33:39Z<p>Mkorcz: </p>
<hr />
<div>Fun in the snow. Lab trip to lake Tahoe.[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]][[Image:007.jpeg]]<br />
[[Image:008.jpeg]][[Image:009.jpeg]][[Image:010.jpeg]][[Image:011.jpeg]][[Image:012.jpeg]][[Image:013.jpeg]][[Image:014.jpeg]][[Image:015.jpeg]][[Image:016.jpeg]][[Image:017.jpeg]][[Image:018.jpeg]][[Image:019.jpeg]][[Image:020.jpeg]]<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4344Shoichet Lab Photos2010-10-13T19:27:02Z<p>Mkorcz: </p>
<hr />
<div>Fun in the snow. Lab trip to lake Tahoe.[[Image:001.jpeg]][[Image:002.jpeg]][[Image:003.jpeg]][[Image:004.jpeg]][[Image:005.jpeg]][[Image:006.jpeg]]<br />
<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4343Shoichet Lab Photos2010-10-13T19:19:03Z<p>Mkorcz: </p>
<hr />
<div>Fun in the snow. Lab trip to lake Tahoe.<br />
<br />
<br />
'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorczhttp://wiki.docking.org/index.php?title=Shoichet_Lab_Photos&diff=4342Shoichet Lab Photos2010-10-12T01:29:20Z<p>Mkorcz: </p>
<hr />
<div>'''Twin days''': when you spend enough time together, you start to dress alike.<br />
[[Image:Twins.jpg]] [[Image:twins2.jpg]]</div>Mkorcz