Using thin spheres in DOCK3.7 - Revision history

Frodo: asdf

2024-05-25T00:21:13Z

asdf

← Older revision		Revision as of 00:21, 25 May 2024
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	* parameter scanning.		* parameter scanning.
	[[how to do parameter scanning]]		[[how to do parameter scanning]]

			[[Category:Spheres]]
			[[Category:DOCK]]

Dudenko at 12:41, 4 September 2019

2019-09-04T12:41:10Z

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	--ts_dist_to_lig=TS_DIST_TO_LIG		--ts_dist_to_lig=TS_DIST_TO_LIG
	for both low dielectric thin spheres and ligand		for both low dielectric thin spheres and ligand
	~~desolovation~~, distance from ligand to keep spheres		desolvation, distance from ligand to keep spheres
	(default: 2.0)		(default: 2.0)

Rstein at 16:58, 28 August 2019

2019-08-28T16:58:42Z

← Older revision		Revision as of 16:58, 28 August 2019
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	If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", ranging from 1-10, depending on how small your radius is. You can check your protein preparation using this tutorial:		If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", ranging from 1-10, depending on how small your radius is. You can check your protein preparation using this tutorial:

	http://wiki.docking.org/index.php~~?title=Protein_Target_Preparation~~		http://wiki.docking.org/index.php/Protein_Target_Preparation_Updated

Rstein at 18:09, 22 April 2019

2019-04-22T18:09:48Z

← Older revision		Revision as of 18:09, 22 April 2019
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	If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", ~~e.g.~~ 1.2-~~1.5~~. You can check your protein preparation using this tutorial:		If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", ranging from 1-10, depending on how small your radius is. You can check your protein preparation using this tutorial:

	http://wiki.docking.org/index.php?title=Protein_Target_Preparation		http://wiki.docking.org/index.php?title=Protein_Target_Preparation

Rstein at 23:03, 16 April 2019

2019-04-16T23:03:37Z

← Older revision		Revision as of 23:03, 16 April 2019
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	python /mnt/nfs/home/rstein/zzz.github/DOCK/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_to_lig 4.0 --mstsDensity 1.2 -v > logfile		python /mnt/nfs/home/rstein/zzz.github/DOCK/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_to_lig 4.0 --mstsDensity 1.2 -v > logfile

	~~If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", e.g. 1.2-1.5.~~

	Another example command:		Another example command:

	$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --useThinSphLdsflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_lds 0.3 --ts_radius_lds 0.3 --ts_dist_to_lig 4.0 --mstsDensity 1.2 -v		$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --useThinSphLdsflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_lds 0.3 --ts_radius_lds 0.3 --ts_dist_to_lig 4.0 --mstsDensity 1.2 -v


			If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", e.g. 1.2-1.5. You can check your protein preparation using this tutorial:

			http://wiki.docking.org/index.php?title=Protein_Target_Preparation

Rstein at 20:08, 16 April 2019

2019-04-16T20:08:19Z

← Older revision		Revision as of 20:08, 16 April 2019
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	For newer versions of DOCK there are new flags in the blastermaster program for control thinsphere generation.		For newer versions of DOCK there are new flags in the blastermaster program for control thinsphere generation.

	For thin spheres use ~~trent~~'s version of blastermaster (~~for now, this will be~~ pushed to the main version ~~in the future~~):		For thin spheres use Reed's version of blastermaster (This has also been pushed to the main version):

	/nfs/home/~~tbalius~~/zzz.github/DOCK/proteins/blastermaster/blastermaster.py		/mnt/nfs/home/rstein/zzz.github/DOCK/proteins/blastermaster/blastermaster.py


	here are the important thinsphere parameters:		here are the important thinsphere parameters:
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	here is an example command:		here is an example command:
	python /mnt/nfs/home/~~tbalius~~/zzz.github/DOCK/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_to_lig 4.0 --mstsDensity 0.2 -v > logfile
	$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --useThinSphLdsflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_lds 0.3 --ts_radius_lds 0.3 --ts_dist_to_lig 4.0 --mstsDensity 0.2 -v		python /mnt/nfs/home/rstein/zzz.github/DOCK/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_to_lig 4.0 --mstsDensity 1.2 -v > logfile

			If you check your spheres and they are discontinuous, run blastermaster again with a higher "mstsDensity", e.g. 1.2-1.5.

			Another example command:

			$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --useThinSphLdsflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_lds 0.3 --ts_radius_lds 0.3 --ts_dist_to_lig 4.0 --mstsDensity 1.2 -v

TBalius: /* Tutorial for using Thin Spheres in DOCK 3.7.1rc1 */

2018-07-31T18:02:55Z

Tutorial for using Thin Spheres in DOCK 3.7.1rc1

← Older revision		Revision as of 18:02, 31 July 2018
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	Here, the -d flag allows us to pass the program a scalar to modify the density of the surface points.		Here, the -d flag allows us to pass the program a scalar to modify the density of the surface points.
	For example, with a -d set to 1.0 the density is will be 5.42 pts/sq.A, while with a -d 0.2, we will get a density of 1.18 pts/sq.A.		For example, with a -d set to 1.0 the density will be 5.42 pts/sq.A, while with a -d 0.2, we will get a density of 1.18 pts/sq.A.

	Instead, you could copy the molecular surface of the original surface (this is OK for small sites):		Instead, you could copy the molecular surface of the original surface (this is OK for small sites):

TBalius: /* Tutorial for using Thin Spheres in DOCK 3.7 */

2018-04-12T16:45:16Z

Tutorial for using Thin Spheres in DOCK 3.7

← Older revision		Revision as of 16:45, 12 April 2018
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	==Tutorial for using Thin Spheres in DOCK 3.7==		==Tutorial for using Thin Spheres in DOCK 3.7.1rc1==

	Written by Trent E. Balius, 2016/11/03.		Written by Trent E. Balius, 2016/11/03.

TBalius at 16:43, 12 April 2018

2018-04-12T16:43:19Z

← Older revision		Revision as of 16:43, 12 April 2018
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	For newer versions of DOCK there are new flags ~~to Blaster master to~~ control thinsphere generation.		For newer versions of DOCK there are new flags in the blastermaster program for control thinsphere generation.

			For thin spheres use trent's version of blastermaster (for now, this will be pushed to the main version in the future):

			/nfs/home/tbalius/zzz.github/DOCK/proteins/blastermaster/blastermaster.py

			here are the important thinsphere parameters:

			--mstsDensity=MSTSDENSITY
			molecular surface denisty for thinspheres (default:
			1.0)
			--useThinSphEleflag if flag is given, use thinspheres in qnifft
			calculation (default: False) Not tested with
			multigrid code.
			--useThinSphLdsflag if flag is given, use thinspheres in ligand
			desolvation calculation (default: False) Not tested
			with multigrid code.
			--ts_dist_ele=TS_DIST_ELE
			for low dielectric thin spheres, distance to protein
			surface (default: 1.0)
			--ts_radius_ele=TS_RADIUS_ELE
			for low dielectric thin spheres, radius of spheres
			(default: 1.0)
			--ts_dist_lds=TS_DIST_LDS
			for ligand desolvation thin spheres, distance to
			protein surface (default: 1.0)
			--ts_radius_lds=TS_RADIUS_LDS
			for ligand desolvation thin spheres, radius of spheres
			(default: 1.0)
			--ts_dist_to_lig=TS_DIST_TO_LIG
			for both low dielectric thin spheres and ligand
			desolovation, distance from ligand to keep spheres
			(default: 2.0)

			here is an example command:
			python /mnt/nfs/home/tbalius/zzz.github/DOCK/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_to_lig 4.0 --mstsDensity 0.2 -v > logfile
			$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --useThinSphEleflag --useThinSphLdsflag --ts_dist_ele 1.0 --ts_radius_ele 1.0 --ts_dist_lds 0.3 --ts_radius_lds 0.3 --ts_dist_to_lig 4.0 --mstsDensity 0.2 -v


	For DOCK3.7.1rc1 and older thinspheres have to be generated manually, e.g. by do the following:		For DOCK3.7.1rc1 and older thinspheres have to be generated manually, e.g. by do the following:

TBalius at 17:53, 11 April 2018

2018-04-11T17:53:00Z

← Older revision		Revision as of 17:53, 11 April 2018
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			For newer versions of DOCK there are new flags to Blaster master to control thinsphere generation.

			For DOCK3.7.1rc1 and older thinspheres have to be generated manually, e.g. by do the following:


	==Tutorial for using Thin Spheres in DOCK 3.7==		==Tutorial for using Thin Spheres in DOCK 3.7==