Pymol

Overview

A molecular visualisation tool.

Restrictions on use

Previously we had an educational-use-only version installed for usage in accordance with the policy on the software vendor website. Usage of this software was restricted to one research group. However this version no longer works on the CSF.

Hence we have compiled the open-source version of PyMOL. This doesn’t have all of the features of the commerical/educational release but can be used by any CSF user.

Version 2.3.0 (open-source) is installed on CSF3.

Set up procedure

You will need to connect to CSF3 using ssh -X to have the display exported to your local machine.

You should then load the pymol module:

module load apps/gcc/pymol/2.3.0

Running the application

The software is launched using the command pymol. It can be run interactively (via its GUI) or in batch via the usual job-script method. Examples are given below. To see what command-line flags are available, run the following command on the login node after loading the modulefile:

pymol --help

Normal use of pymol should not use the login node – it must be run on a compute node.

Interactive Usage

If you need to run the software interactively you must do so via a compute node using qrsh e.g:

qrsh -l short -V -cwd pymol

Alternatively, log in to the compute node first and then setup and run pymol

qrsh -l short
 #
 # Wait until you have been logged in to t a compute node, then:
module load apps/gcc/pymol/2.3.0
pymol

Batch Usage

To run pymol in a batch job, without the GUI, create a jobscript similar to the following:

#!/bin/bash --login
#$ -cwd
#$ -pe smp.pe 8        # Optional line (e.g., use 8 cores). Delete line for a serial job.
module load apps/gcc/pymol/2.3.0

pymol -c -d "set max_threads, $NSLOTS" -r myscript.py
                               #
                               # This will tell pymol to use the number of cores
                               # specified above (or 1 for a serial job)

Submit you job to the batch system using

qsub myjobscript

where myjobscript is the name of your jobscript file.

Further info

The pymol website has a variety of resources available including a user maintained wiki.