DOCK 3.7 2015/04/15 abl1 Tutorial - Revision history

Frodo: asdf

2023-10-19T21:05:53Z

asdf

← Older revision		Revision as of 21:05, 19 October 2023
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	To modify spheres: first, convert them to pdb format; then, visualize them in your favorite program (pymol, chimera, etc.); then, delete, move, or add atoms to this file; and finally convert it back to the sph format.		To modify spheres: first, convert them to pdb format; then, visualize them in your favorite program (pymol, chimera, etc.); then, delete, move, or add atoms to this file; and finally convert it back to the sph format.

	As discussed above [[http://wiki.~~bkslab~~.org/index.php/DOCK_3.7_2015/04/15_abl1_Tutorial#Visualize_the_docking_spheres]], you may use doshowsph.csh to convert the spheres to pdb format.		As discussed above [[http://wiki.docking.org/index.php/DOCK_3.7_2015/04/15_abl1_Tutorial#Visualize_the_docking_spheres]], you may use doshowsph.csh to convert the spheres to pdb format.

	Here is the program that will convert a pdb file into a sphere file (this program take 2 inputs: name of pdbfile to convert and the name of the sphere file that you want to create.).		Here is the program that will convert a pdb file into a sphere file (this program take 2 inputs: name of pdbfile to convert and the name of the sphere file that you want to create.).

2018-06-05T15:56:18Z

← Older revision		Revision as of 15:56, 5 June 2018
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	This tutorial use the 3.7.2 beta version of dock release on April 17, 2015. ~~this~~ tutorial is now superseded by[[DOCK 3.7 2018/06/05 abl1 Tutorial]].		This tutorial use the 3.7.2 beta version of dock release on April 17, 2015. This tutorial is now superseded by[[DOCK 3.7 2018/06/05 abl1 Tutorial]].

	This is for a Linux environment and the scripts assume that you are running on SGE queuing system.		This is for a Linux environment and the scripts assume that you are running on SGE queuing system.

2018-06-05T15:56:06Z

← Older revision		Revision as of 15:56, 5 June 2018
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	This tutorial use the 3.7.2 beta version of dock release on April 17, 2015.		This tutorial use the 3.7.2 beta version of dock release on April 17, 2015. this tutorial is now superseded by[[DOCK 3.7 2018/06/05 abl1 Tutorial]].

	This is for a Linux environment and the scripts assume that you are running on SGE queuing system.		This is for a Linux environment and the scripts assume that you are running on SGE queuing system.

2018-06-04T17:15:23Z

Modify matching spheres

← Older revision		Revision as of 17:15, 4 June 2018
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	As discussed above [[http://wiki.bkslab.org/index.php/DOCK_3.7_2015/04/15_abl1_Tutorial#Visualize_the_docking_spheres]], you may use doshowsph.csh to convert the spheres to pdb format.		As discussed above [[http://wiki.bkslab.org/index.php/DOCK_3.7_2015/04/15_abl1_Tutorial#Visualize_the_docking_spheres]], you may use doshowsph.csh to convert the spheres to pdb format.

	Here is the ~~script~~ that will convert a pdb file into a sphere file.		Here is the program that will convert a pdb file into a sphere file (this program take 2 inputs: name of pdbfile to convert and the name of the sphere file that you want to create.).
	$DOCKBASE/proteins/pdbtosph/bin/pdbtosph		$DOCKBASE/proteins/pdbtosph/bin/pdbtosph

			for example:
			$DOCKBASE/proteins/pdbtosph/bin/pdbtosph matching_spheres_mod.pdb matching_spheres_mod.sph

2018-05-02T21:50:50Z

combine scores and poses

← Older revision		Revision as of 21:50, 2 May 2018
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	Write this file as 0004.combineScoresAndPoses.csh. This script combines your docking runs (for ligands and decoys) and stores them in the extract_all.txt file. It also creates a .mol2 file containing all top scoring poses for each ligand/decoy.		Write this file as 0004.combineScoresAndPoses.csh. This script combines your docking runs (for ligands and decoys) and stores them in the extract_all.txt file. It also creates a .mol2 file containing all top scoring poses for each ligand/decoy.

			Note that if you used the alternative (which is preferred) submission in the above step, then you will need to modify the directory structure in the below script.

			From:
			${mountdir}/${pdbname}/ligands-decoys/${db_type}/allChunksCombined
			To:
			${mountdir}/${pdbname}/${db_type}/allChunksCombined

	#!/bin/csh		#!/bin/csh

2017-04-26T22:00:41Z

Virtual Screening

← Older revision		Revision as of 22:00, 26 April 2017
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	python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 count		python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 count

			The file /nfs/work/tbalius/database_ph4/frags.txt should be changed to that you downloaded from ZINC.

			The above script has 5 parameters:
			:(1) path where directories will be located (present directory);
			:(2) prefix name of the directories;
			:(3) the file that contains the db2 files locations;
			:(4) the number of directories to be created; and
			:(5) the type of run: count (evenly distributes the db2 file among the dirs, this is much faster than the other options), size (It will try and make the directory of equal size), or both (will try and satisfy both criteria).

	Note that this script is avable in later beta versons of DOCK3.7.		Note that this script is avable in later beta versons of DOCK3.7.

2017-04-24T17:31:17Z

← Older revision		Revision as of 17:31, 24 April 2017
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	This is for a Linux environment and the scripts assume that you are running on SGE queuing system.		This is for a Linux environment and the scripts assume that you are running on SGE queuing system.

	More information and tutorials ~~are here for~~ [[DOCK_3.7]].		More information and tutorials, see [[DOCK_3.7]].

	== set up directories and get databases ==		== set up directories and get databases ==

2017-04-24T17:30:00Z

← Older revision		Revision as of 17:30, 24 April 2017
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	This is for a Linux environment and the scripts assume that you are running on SGE queuing system.		This is for a Linux environment and the scripts assume that you are running on SGE queuing system.

			More information and tutorials are here for [[DOCK_3.7]].

	== set up directories and get databases ==		== set up directories and get databases ==

2017-04-18T17:52:37Z

set up directories and get databases

← Older revision		Revision as of 17:52, 18 April 2017
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	Create directory called "RotationProject"		Create directory called "RotationProject"

	create a python file called "autodude_db_download.py"		create a python file called "0000.autodude_db_download.py"

	# this gets the database from the autodude webpage		# this gets the database from the autodude webpage

2017-04-18T17:48:47Z

run enrichment calculations

← Older revision		Revision as of 17:48, 18 April 2017
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	#It assumes that ligands and decoys have been pre-prepation (see script blablabla_ToDo) which needs to be run in SF.		#It assumes that ligands and decoys have been pre-prepation (see script blablabla_ToDo) which needs to be run in SF.

	# filedir is where your rec.pdb ~~and~~ xtal-lig.pdb and dockfiles directory live		# $filedir/$pdbname is where your rec.pdb, xtal-lig.pdb, INDOCK, and dockfiles directory live
	set filedir = "/mnt/nfs/home/rstein/RotationProject" #CHANGE THIS		set filedir = "/mnt/nfs/home/rstein/RotationProject" #CHANGE THIS
	# this is where the work is done:		# this is where the work is done: