Removing Spheres (The Chase Method) - Revision history

Rstein at 20:17, 27 May 2020

2020-05-27T20:17:45Z

← Older revision		Revision as of 20:17, 27 May 2020
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	The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.		The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.

			NOTE: You need to run this script in the directory outside of {YOUR_DOCK_DIR}

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404

Rstein at 20:17, 27 May 2020

2020-05-27T20:17:16Z

Rstein at 19:27, 27 May 2020

2020-05-27T19:27:47Z

Rstein at 18:51, 21 May 2020

2020-05-21T18:51:46Z

← Older revision		Revision as of 18:51, 21 May 2020
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	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404

	If you want to include more atom coordinates, ~~include~~ more x,y,z coordinates.		If you want to include more atom coordinates, just continue adding more x,y,z coordinates after the -c flag

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 58.038 47.323 12.300		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 58.038 47.323 12.300

Rstein at 18:51, 21 May 2020

2020-05-21T18:51:21Z

← Older revision		Revision as of 18:51, 21 May 2020
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	http://wiki.docking.org/index.php/Protein_Target_Preparation_Updated#Checking_Your_Protein_Preparation		http://wiki.docking.org/index.php/Protein_Target_Preparation_Updated#Checking_Your_Protein_Preparation


	If satisfied with your spheres, run the second script to recalculate the "hydrogen" and "heavy" ligand desolvation grids. This script submits the SOLVMAP calculation to the queue. It requires the radius of your ligand desolvation spheres for the SOLVMAP calculation. As before you need the "working/" subdirectory containing the "box" file and the newly created "rec.crg.lds.pdb" file from the previous script. If you already have "hydrogen/" and "heavy/" subdirectories within your "working/" directory, it will ask you to either move or delete these.		If satisfied with your spheres, run the second script to recalculate the "hydrogen" and "heavy" ligand desolvation grids. This script submits the SOLVMAP calculation to the queue. It requires the radius of your ligand desolvation spheres for the SOLVMAP calculation. As before you need the "working/" subdirectory containing the "box" file and the newly created "rec.crg.lds.pdb" file from the previous script. If you already have "hydrogen/" and "heavy/" subdirectories within your "working/" directory, it will ask you to either move or delete these.

Rstein at 18:50, 21 May 2020

2020-05-21T18:50:56Z

← Older revision		Revision as of 18:50, 21 May 2020
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	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404


	If you want to include more atom coordinates, include more x,y,z coordinates.		If you want to include more atom coordinates, include more x,y,z coordinates.

Rstein at 18:49, 21 May 2020

2020-05-21T18:49:58Z

← Older revision		Revision as of 18:49, 21 May 2020
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	Once you have run this script, you can visualize your spheres by following this tutorial:		Once you have run this script, you can visualize your spheres by following this tutorial:

			http://wiki.docking.org/index.php/Protein_Target_Preparation_Updated#Checking_Your_Protein_Preparation

Rstein at 18:41, 21 May 2020

2020-05-21T18:41:18Z

← Older revision		Revision as of 18:41, 21 May 2020
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	Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {YOUR_DOCK_DIR/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:		Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {YOUR_DOCK_DIR/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:

	cp {YOUR_DOCK_DIR/working/hydrogen/ligand.desolv.hydrogen dockfiles/.		cp {YOUR_DOCK_DIR/working/hydrogen/ligand.desolv.hydrogen dockfiles/.
	cp {YOUR_DOCK_DIR/working/heavy/ligand.desolv.heavy dockfiles/.		cp {YOUR_DOCK_DIR/working/heavy/ligand.desolv.heavy dockfiles/.

Rstein: Created page with "These scripts are used for removing ligand desolvation spheres around atom(s) of interest. This is to decrease the desolvation cost in a targeted way. 5/21/2020 Pioneered by ..."

2020-05-21T18:40:50Z

Created page with "These scripts are used for removing ligand desolvation spheres around atom(s) of interest. This is to decrease the desolvation cost in a targeted way. 5/21/2020 Pioneered by ..."

New page

These scripts are used for removing ligand desolvation spheres around atom(s) of interest. This is to decrease the desolvation cost in a targeted way.

5/21/2020
Pioneered by Chase Webb.
Scripts written by Reed Stein.

The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.

python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404

If you want to include more atom coordinates, include more x,y,z coordinates.

python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 58.038 47.323 12.300

To increase the radius around the atoms that you want to remove ligand desolvation spheres from, include the -d flag:

python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 -d 5

Once you have run this script, you can visualize your spheres by following this tutorial:

If satisfied with your spheres, run the second script to recalculate the "hydrogen" and "heavy" ligand desolvation grids. This script submits the SOLVMAP calculation to the queue. It requires the radius of your ligand desolvation spheres for the SOLVMAP calculation. As before you need the "working/" subdirectory containing the "box" file and the newly created "rec.crg.lds.pdb" file from the previous script. If you already have "hydrogen/" and "heavy/" subdirectories within your "working/" directory, it will ask you to either move or delete these.

If you had a ligand desolvation sphere radius of 0.1 Å, use the following command:

python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_make_ld_dirs.py -p {YOUR_DOCK_DIR} -r 0.1

FINAL STEP!
Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {YOUR_DOCK_DIR/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:

cp {YOUR_DOCK_DIR/working/hydrogen/ligand.desolv.hydrogen dockfiles/.
cp {YOUR_DOCK_DIR/working/heavy/ligand.desolv.heavy dockfiles/.

← Older revision		Revision as of 20:17, 27 May 2020
Line 7:		Line 7:
	The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.		The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {~~FULL_PATH_TO_DOCK_DIR~~} -c 42.301 43.502 48.404		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404

	If you want to include more atom coordinates, just continue adding more x,y,z coordinates after the -c flag		If you want to include more atom coordinates, just continue adding more x,y,z coordinates after the -c flag

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {~~FULL_PATH_TO_DOCK_DIR~~} -c 42.301 43.502 48.404 58.038 47.323 12.300		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 58.038 47.323 12.300

	To increase the radius around the atoms that you want to remove ligand desolvation spheres from, include the -d flag:		To increase the radius around the atoms that you want to remove ligand desolvation spheres from, include the -d flag:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {~~FULL_PATH_TO_DOCK_DIR~~} -c 42.301 43.502 48.404 -d 5		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 -d 5

	Once you have run this script, you can visualize your spheres by following this tutorial:		Once you have run this script, you can visualize your spheres by following this tutorial:
Line 25:		Line 25:
	If you had a ligand desolvation sphere radius of 0.1 Å, use the following command:		If you had a ligand desolvation sphere radius of 0.1 Å, use the following command:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_make_ld_dirs.py -p {~~FULL_PATH_TO_DOCK_DIR~~} -r 0.1		python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_make_ld_dirs.py -p {YOUR_DOCK_DIR} -r 0.1

	FINAL STEP!		FINAL STEP!
	Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {~~FULL_PATH_TO_DOCK_DIR~~/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:		Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {YOUR_DOCK_DIR}/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:

	cp {~~FULL_PATH_TO_DOCK_DIR~~/working/hydrogen/ligand.desolv.hydrogen dockfiles/.		cp {YOUR_DOCK_DIR}/working/hydrogen/ligand.desolv.hydrogen dockfiles/.
	cp {~~FULL_PATH_TO_DOCK_DIR~~/working/heavy/ligand.desolv.heavy dockfiles/.		cp {YOUR_DOCK_DIR}/working/heavy/ligand.desolv.heavy dockfiles/.

← Older revision		Revision as of 19:27, 27 May 2020
Line 7:		Line 7:
	The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.		The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {~~YOUR_DOCK_DIR~~} -c 42.301 43.502 48.404		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {FULL_PATH_TO_DOCK_DIR} -c 42.301 43.502 48.404

	If you want to include more atom coordinates, just continue adding more x,y,z coordinates after the -c flag		If you want to include more atom coordinates, just continue adding more x,y,z coordinates after the -c flag

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {~~YOUR_DOCK_DIR~~} -c 42.301 43.502 48.404 58.038 47.323 12.300		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {FULL_PATH_TO_DOCK_DIR} -c 42.301 43.502 48.404 58.038 47.323 12.300

	To increase the radius around the atoms that you want to remove ligand desolvation spheres from, include the -d flag:		To increase the radius around the atoms that you want to remove ligand desolvation spheres from, include the -d flag:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {~~YOUR_DOCK_DIR~~} -c 42.301 43.502 48.404 -d 5		python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {FULL_PATH_TO_DOCK_DIR} -c 42.301 43.502 48.404 -d 5

	Once you have run this script, you can visualize your spheres by following this tutorial:		Once you have run this script, you can visualize your spheres by following this tutorial:
Line 25:		Line 25:
	If you had a ligand desolvation sphere radius of 0.1 Å, use the following command:		If you had a ligand desolvation sphere radius of 0.1 Å, use the following command:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_make_ld_dirs.py -p {~~YOUR_DOCK_DIR~~} -r 0.1		python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_make_ld_dirs.py -p {FULL_PATH_TO_DOCK_DIR} -r 0.1

	FINAL STEP!		FINAL STEP!
	Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {~~YOUR_DOCK_DIR~~/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:		Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {FULL_PATH_TO_DOCK_DIR/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:

	cp {~~YOUR_DOCK_DIR~~/working/hydrogen/ligand.desolv.hydrogen dockfiles/.		cp {FULL_PATH_TO_DOCK_DIR/working/hydrogen/ligand.desolv.hydrogen dockfiles/.
	cp {~~YOUR_DOCK_DIR~~/working/heavy/ligand.desolv.heavy dockfiles/.		cp {FULL_PATH_TO_DOCK_DIR/working/heavy/ligand.desolv.heavy dockfiles/.