Blastermaster (pydock3 script) - Revision history

Khtang: /* Gimel */

2024-07-18T19:08:46Z

Gimel

← Older revision		Revision as of 19:08, 18 July 2024
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	Only nodes other than ''gimel'' itself are supported, e.g., ''gimel2''.		Only nodes other than ''gimel'' itself are supported, e.g., ''gimel2''.

	ssh ~~gimel5~~		ssh gimel2
	source /nfs/soft/ian/python3.8.5.sh		source /nfs/soft/ian/python3.8.5.sh

Khtang: /* Gimel */

2024-07-18T19:08:27Z

Gimel

← Older revision		Revision as of 19:08, 18 July 2024
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	=== Gimel ===		=== Gimel ===

	Only nodes other than ''gimel'' itself are supported, e.g., ''~~gimel5~~''.		Only nodes other than ''gimel'' itself are supported, e.g., ''gimel2''.

	ssh gimel5		ssh gimel5

Frodo: asdf

2024-05-02T17:48:12Z

asdf

← Older revision		Revision as of 17:48, 2 May 2024
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	This will execute the many blastermaster subroutines in sequence. The state of the program will be printed to standard output as it runs.		This will execute the many blastermaster subroutines in sequence. The state of the program will be printed to standard output as it runs.

			[[Category:DOCK 3.8]]
			[[Category:Documentation]]
			[[Category:Blaster]]

Ianscottknight at 07:49, 12 December 2023

2023-12-12T07:49:01Z

← Older revision		Revision as of 07:49, 12 December 2023
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	== Note for UCSF Shoichet Lab members ==		== Note for UCSF Shoichet Lab members ==

	''pydock3'' is already installed on the following clusters. You can source the provided Python environment scripts to expose the ''pydock3'' ~~executable~~:		''pydock3'' is already installed on the following clusters. You can source the provided Python environment scripts to expose the ''pydock3'' command:

	=== Wynton ===		=== Wynton ===

Ianscottknight at 18:52, 9 June 2023

2023-06-09T18:52:21Z

← Older revision		Revision as of 18:52, 9 June 2023
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	source /nfs/soft/ian/python3.8.5.sh		source /nfs/soft/ian/python3.8.5.sh

	== ''~~init~~'' ==		== ''new'' ==

	First you need to create the file structure for your blastermaster job. To do so, simply type		First you need to create the file structure for your blastermaster job. To do so, simply type

	pydock3 blastermaster - ~~init~~		pydock3 blastermaster - new

	By default, the job directory is named ''blastermaster_job''. To specify a different name, type		By default, the job directory is named ''blastermaster_job''. To specify a different name, type

	pydock3 blastermaster - ~~init~~ <JOB_DIR_NAME>		pydock3 blastermaster - new <JOB_DIR_NAME>

	The job directory contains two sub-directories:		The job directory contains two sub-directories:
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	* ''rec.pdb''		* ''rec.pdb''
			* ''rec.crg.pdb''
	* ''xtal-lig.pdb''		* ''xtal-lig.pdb''
	* ''rec.crg.pdb''
	* ''reduce_wwPDB_het_dict.txt''		* ''reduce_wwPDB_het_dict.txt''
	* ''filt.params''		* ''filt.params''

Ianscottknight at 23:40, 11 October 2022

2022-10-11T23:40:43Z

← Older revision		Revision as of 23:40, 11 October 2022
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	''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand.		''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand.

			== Note for UCSF Shoichet Lab members ==

			''pydock3'' is already installed on the following clusters. You can source the provided Python environment scripts to expose the ''pydock3'' executable:

			=== Wynton ===

			source /wynton/group/bks/soft/python_envs/python3.8.5.sh

			=== Gimel ===

			Only nodes other than ''gimel'' itself are supported, e.g., ''gimel5''.

			ssh gimel5
			source /nfs/soft/ian/python3.8.5.sh

	== ''init'' ==		== ''init'' ==

Ianscottknight: Created page with "''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand. == ''init'' == First you need to create the file structure for y..."

2022-09-02T08:10:54Z

Created page with "''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand. == ''init'' == First you need to create the file structure for y..."

New page

''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand.

== ''init'' ==

First you need to create the file structure for your blastermaster job. To do so, simply type

pydock3 blastermaster - init

By default, the job directory is named ''blastermaster_job''. To specify a different name, type

pydock3 blastermaster - init <JOB_DIR_NAME>

The job directory contains two sub-directories:
# ''working'': input files, intermediate blaster files, sub-directories for individual blastermaster subroutines
# ''dockfiles'': output files (DOCK parameter files & INDOCK)

If your current working directory contains any of the following files, then they will be automatically copied into the working directory within the created job directory. This feature is intended to simplify the process of configuring the blastermaster job.

* ''rec.pdb''
* ''xtal-lig.pdb''
* ''rec.crg.pdb''
* ''reduce_wwPDB_het_dict.txt''
* ''filt.params''
* ''radii''
* ''amb.crg.oxt''
* ''vdw.siz''
* ''delphi.def''
* ''vdw.parms.amb.mindock''
* ''prot.table.ambcrg.ambH''

Only the following are required. Default versions / generated versions of the others will be used instead if they are not detected.
* ''rec.pdb''
* ''xtal-lig.pdb''

If you would like to use files not present in your current working directory, then copy them into your job's working directory, e.g.:
cp <FILE_PATH> <JOB_DIR_NAME>/working/

Finally, configure the ''blastermaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of blastermaster.

== ''run'' ==

Once your job has been configured to your liking, navigate to the the job directory and run blastermaster:
cd <JOB_DIR_NAME>
pydock3 blastermaster - run

This will execute the many blastermaster subroutines in sequence. The state of the program will be printed to standard output as it runs.