Blastermaster (pydock3 script)

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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:


 source /wynton/group/bks/soft/python_envs/


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

ssh gimel5
source /nfs/soft/ian/


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:

  1. working: input files, intermediate blaster files, sub-directories for individual blastermaster subroutines
  2. 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.


Once your job has been configured to your liking, navigate to the the job directory and run blastermaster:

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.