DOCK 3.7 2014/09/25 FXa Tutorial - Revision history

TBalius: /* This part of the tutorial uses the GIST development version of DOCK */

2016-04-26T23:37:27Z

This part of the tutorial uses the GIST development version of DOCK

2014-09-26T17:45:03Z

← Older revision		Revision as of 17:45, 26 September 2014
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	Tools/		Tools/

	[[File: Veiwdock.FXa.frag.top200.png]]		[[File: Veiwdock.FXa.frag.top200.png\|thumb\|center\|375px\| Chimera Viewdock session for top 200 Frags. ]]

	==This part of the tutorial uses the GIST development version of DOCK==		==This part of the tutorial uses the GIST development version of DOCK==

2014-09-26T17:38:08Z

pose visualization

← Older revision		Revision as of 17:38, 26 September 2014
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	=== pose visualization ===		=== pose visualization ===

	~~use~~ chimera:		Use chimera Veiwdock modual:

			Tools/

			[[File: Veiwdock.FXa.frag.top200.png]]

	==This part of the tutorial uses the GIST development version of DOCK==		==This part of the tutorial uses the GIST development version of DOCK==

2014-09-26T13:06:35Z

Receptor Preparation

← Older revision		Revision as of 13:06, 26 September 2014
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	2.a. this script will run blastermaster.py:		2.a. this script will run blastermaster.py:

	cat ~~~cnnguyen~~/FactorXa/dock_tutorial/0002.blastermaster.csh ~~\| more~~		cat ~/FactorXa/dock_tutorial/0002.blastermaster.csh
	#!/bin/csh		#!/bin/csh
			# Written by Trent Balius, 2014.
	# This script runs Ryan's blastermaster python masterscript for generating everything that dock needs, i.e. grids, spheres		# This script runs Ryan's blastermaster python masterscript for generating everything that dock needs, i.e. grids, spheres
	# Run on sgehead as jobs are submitted to the queue		# Run on sgehead as jobs are submitted to the queue
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	change sphere placement.		change sphere placement.
	modify receptor changes.		modify receptor changes.
	modify sidechain rotomers.		modify sidechain rotomers.

	=== pose visualization ===		=== pose visualization ===

2014-09-26T13:05:18Z

This part of the tutorial uses the GIST development version of DOCK

← Older revision		Revision as of 13:05, 26 September 2014
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	Three ligand files are needed for rescoring:		Three ligand files are needed for rescoring:

	1. poses.mol2.gz		1. poses.mol2.gz

	2. amsol_desov.txt.gz		2. amsol_desov.txt.gz

	3. vdw.txt.gz		3. vdw.txt.gz

2014-09-26T13:05:01Z

This part of the tutorial uses the GIST development version of DOCK

← Older revision		Revision as of 13:05, 26 September 2014
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	This chimera script might help.		This chimera script might help.

			Rescoring with GIST dev version.

			Three ligand files are needed for rescoring:
			1. poses.mol2.gz
			2. amsol_desov.txt.gz
			3. vdw.txt.gz

2014-09-26T12:56:46Z

← Older revision		Revision as of 12:56, 26 September 2014
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	3. Submit enrichment calculation		3. Submit enrichment calculation
	3.1 First you need a database. see the database generation section.		3.1 First you need a database. see the database generation section [[DOCK_3.7_2014/09/25_FXa_Tutorial#making_ligand_databases.]].

	4. Process enrichment caluclations: Genereate Log-ajusted ROC curves and caluclate Log-ajusted AUC values.		4. Process enrichment caluclations: Genereate Log-ajusted ROC curves and caluclate Log-ajusted AUC values.

2014-09-26T12:55:13Z

@@ Line 246: / Line 246: @@
   #       ligand.desolv.hydroge
-=== pose visualization ==
+. Submit enrichment calculation
 use chimera:

2014-09-26T12:49:14Z

Receptor Preparation

← Older revision		Revision as of 12:49, 26 September 2014
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	1. Splite your pdb into a rec.pdb and xtal-lig.pdb.		1. Splite your pdb into a rec.pdb and xtal-lig.pdb.

	1.a you can do this by running this script:		1.a you can do this by running this script:

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	2. Generate spheres and grids:		2. Generate spheres and grids:

	2.a. this script will run blastermaster.py:		2.a. this script will run blastermaster.py:

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	# spheres		# spheres
	# matching_spheres.sph		# matching_spheres.sph

			2.b. the blastermaster script will generate spheres by calling sphgen, converting ligand into sphere, and processing them with other scripts.


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	This image read shows the spheres in the rec.crg.pdb. This is the file on which qnifft runs the PB calculation.		This image read shows the spheres in the rec.crg.pdb. This is the file on which qnifft runs the PB calculation.

			2.c. The Script blastermaster.py will also produces grids.

			# grids
			# trim.electrostatics.phi
			# vdw.vdw
			# vdw.bmp
			# ligand.desolv.heavy
			# ligand.desolv.hydroge

	=== pose visualization ==		=== pose visualization ==

2014-09-26T12:43:57Z

Receptor Preparation

@@ Line 79: / Line 79: @@
 === Receptor Preparation ===
-# Splite your pdb into a rec.pdb and xtal-lig.pdb.
+. Splite your pdb into a rec.pdb and xtal-lig.pdb.
-## you can do this by running this script:
+.a you can do this by running this script:
   cat ~/FactorXa/dock_tutorial/0001.be_balsti_py.csh
@@ Line 150: / Line 150: @@
     endif
   end # system
 The program sphgen will produce spheres that fill the nooks and crannies on the protein surface.