How to do parameter scanning - Revision history

Sevigneron at 15:35, 2 August 2024

2024-08-02T15:35:01Z

← Older revision		Revision as of 15:35, 2 August 2024
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	This will create a new directory called "combo_directories" with docking-ready directories inside. The directories will have the name format "es_{ES_sphere_radius}_ld_{LD_sphere_radius}". "def" refers to grids taken from your ${FULL_ORIGINAL_BLASTERMASTER_PATH} directory.		This will create a new directory called "combo_directories" with docking-ready directories inside. The directories will have the name format "es_{ES_sphere_radius}_ld_{LD_sphere_radius}". "def" refers to grids taken from your ${FULL_ORIGINAL_BLASTERMASTER_PATH} directory.

			If you are going to be docking with DOCK3.8, then the INDOCK files must be inside dockfiles. To set up these directories, run this script instead:

			~svigneron/work_exj/scripts/new_0002_combine_es_ld_grids_into_combos_dock38.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH}

	These directories are now ready for docking.		These directories are now ready for docking.

Matthew O'Meara: add dollar signs to shell variables

2021-09-21T20:04:04Z

add dollar signs to shell variables

← Older revision		Revision as of 20:04, 21 September 2021
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	and run the following command:		and run the following command:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH}		python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH}

	The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:		The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:
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	If you wanted to change all, you could use:		If you wanted to change all, you could use:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH}		python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH}
	-es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4		-es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4

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	Then run the following script to combine the ES/LD grids in all combinations:		Then run the following script to combine the ES/LD grids in all combinations:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0002_combine_es_ld_grids_into_combos.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH}		python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0002_combine_es_ld_grids_into_combos.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH}

	This will create a new directory called "combo_directories" with docking-ready directories inside. The directories will have the name format "es_{ES_sphere_radius}_ld_{LD_sphere_radius}". "def" refers to grids taken from your {FULL_ORIGINAL_BLASTERMASTER_PATH} directory.		This will create a new directory called "combo_directories" with docking-ready directories inside. The directories will have the name format "es_{ES_sphere_radius}_ld_{LD_sphere_radius}". "def" refers to grids taken from your ${FULL_ORIGINAL_BLASTERMASTER_PATH} directory.

	These directories are now ready for docking.		These directories are now ready for docking.

Rstein at 18:02, 29 May 2020

2020-05-29T18:02:29Z

← Older revision		Revision as of 18:02, 29 May 2020
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	Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]		Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]
	3) DMS density: use the -d flag. Default is 10.0 to ensure that the surface is sufficiently coated with spheres when using		3) DMS density: use the -d flag. Default is 10.0 to ensure that the surface is sufficiently coated with spheres when using
	a smaller sphere radii (typically <0.5 Å). This can be reduced to 1.0 if only larger sphere radii are used.		a smaller sphere radii (typically <0.5 Å). This can be reduced to 1.0 if only larger sphere radii are used.
	4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.		4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.

Rstein at 18:02, 29 May 2020

2020-05-29T18:02:15Z

← Older revision		Revision as of 18:02, 29 May 2020
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	2) Radius of ligand desolvation spheres you want to run: use the -ld flag.		2) Radius of ligand desolvation spheres you want to run: use the -ld flag.
	Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]		Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]
	3) DMS density: use the -d flag. Default is 1.0		3) DMS density: use the -d flag. Default is 10.0 to ensure that the surface is sufficiently coated with spheres when using
			a smaller sphere radii (typically <0.5 Å). This can be reduced to 1.0 if only larger sphere radii are used.
	4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.		4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.

Rstein at 17:51, 29 May 2020

2020-05-29T17:51:36Z

← Older revision		Revision as of 17:51, 29 May 2020
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	The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:		The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:
	1) Radius of low dielectric spheres you want to run: use the -es flag. Default radius for electrostatic spheres is [1.0, 1.3, 1.5, 1.7, 1.9]		1) Radius of low dielectric spheres you want to run: use the -es flag.
	2) Radius of ligand desolvation spheres you want to run: use the -ld flag. Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]		Default radius for electrostatic spheres is [1.0, 1.3, 1.5, 1.7, 1.9]
			2) Radius of ligand desolvation spheres you want to run: use the -ld flag.
			Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]
	3) DMS density: use the -d flag. Default is 1.0		3) DMS density: use the -d flag. Default is 1.0
	4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.		4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.
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	If you wanted to change all, you could use:		If you wanted to change all, you could use:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH} -es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4		python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH}
			-es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4

	This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:		This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:

Rstein at 17:50, 29 May 2020

2020-05-29T17:50:09Z

← Older revision		Revision as of 17:50, 29 May 2020
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	and run the following command:		and run the following command:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/~~new_0001_combined_ES_LD_generation~~.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH}		python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH}

	The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:		The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:
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	If you wanted to change all, you could use:		If you wanted to change all, you could use:

	python ~rstein/zzz.scripts/DOCK_prep_scripts/~~new_0001_combined_ES_LD_generation~~.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH} -es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4		python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p {FULL_ORIGINAL_BLASTERMASTER_PATH} -es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4

	This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:		This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:

Rstein: /* Manually Generating ES/LD Combinations */

2020-05-21T19:32:56Z

Manually Generating ES/LD Combinations

← Older revision		Revision as of 19:32, 21 May 2020
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	== Manually Generating ES/LD Combinations ==		== Manually Generating ES/LD Combinations ==

	written by Reed Stein, updated 5/~~21/2020~~ so users can specify different low dielectric and ligand desolvation sphere radii		written by Reed Stein, updated 12/2019 so users can specify different low dielectric and ligand desolvation sphere radii

	To generate different sized low dielectric and ligand desolvation thin sphere combinations, you must first run blastermaster on your protein/ligand of interest. Once this is finished, make a new directory. Change into the new directory		To generate different sized low dielectric and ligand desolvation thin sphere combinations, you must first run blastermaster on your protein/ligand of interest. Once this is finished, make a new directory. Change into the new directory

Rstein at 19:32, 21 May 2020

2020-05-21T19:32:27Z

← Older revision		Revision as of 19:32, 21 May 2020
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	This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:		This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:

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

	Then run the following script to combine the ES/LD grids in all combinations:		Then run the following script to combine the ES/LD grids in all combinations:

Rstein: /* Blastermaster Parameter Scanning */

2020-05-21T19:31:24Z

Blastermaster Parameter Scanning

← Older revision		Revision as of 19:31, 21 May 2020
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	4/16/2019 - this needs to be updated and will result in discontinuous thin spheres at low radii!		4/16/2019 - this needs to be updated and will result in discontinuous thin spheres at low radii!
	Use the tutorial above instead. Or use this link to run blastermaster manually ~~instead~~:		Use the tutorial above instead. Or use this link to run blastermaster manually:

	http://wiki.docking.org/index.php/Using_thin_spheres_in_DOCK3.7		http://wiki.docking.org/index.php/Using_thin_spheres_in_DOCK3.7

Rstein: /* Blastermaster Parameter Scanning */

2020-05-21T19:31:11Z

Blastermaster Parameter Scanning

← Older revision		Revision as of 19:31, 21 May 2020
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	Written by Jiankun Lyu, 2017/01/18		Written by Jiankun Lyu, 2017/01/18

	4/16/2019 - this needs to be updated and will result in discontinuous thin spheres at low radii! Use this link to run blastermaster manually instead:		4/16/2019 - this needs to be updated and will result in discontinuous thin spheres at low radii!
			Use the tutorial above instead. Or use this link to run blastermaster manually instead:

	http://wiki.docking.org/index.php/Using_thin_spheres_in_DOCK3.7		http://wiki.docking.org/index.php/Using_thin_spheres_in_DOCK3.7