Blastermaster (pydock3 script): Difference between revisions
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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'' | ''pydock3'' is already installed on the following clusters. You can source the provided Python environment scripts to expose the ''pydock3'' command: | ||
=== Wynton === | === Wynton === | ||
| Line 11: | Line 11: | ||
=== Gimel === | === Gimel === | ||
Only nodes other than ''gimel'' itself are supported, e.g., '' | Only nodes other than ''gimel'' itself are supported, e.g., ''gimel2''. | ||
ssh | ssh gimel2 | ||
source /nfs/soft/ian/python3.8.5.sh | source /nfs/soft/ian/python3.8.5.sh | ||
== '' | == ''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 - | 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 - | 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'' | ||
* ''reduce_wwPDB_het_dict.txt'' | * ''reduce_wwPDB_het_dict.txt'' | ||
* ''filt.params'' | * ''filt.params'' | ||
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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]] | |||
Latest revision as of 19:08, 18 July 2024
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 command:
Wynton
source /wynton/group/bks/soft/python_envs/python3.8.5.sh
Gimel
Only nodes other than gimel itself are supported, e.g., gimel2.
ssh gimel2 source /nfs/soft/ian/python3.8.5.sh
new
First you need to create the file structure for your blastermaster job. To do so, simply type
pydock3 blastermaster - new
By default, the job directory is named blastermaster_job. To specify a different name, type
pydock3 blastermaster - new <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
- rec.crg.pdb
- xtal-lig.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.