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What is PyMOL?

PyMOL is an open source molecular graphics system with an embedded Python interpreter designed for both real-time visualization of 3D molecular structures and generation of high-quality renderings and animations. Having been created by Warren Lyford DeLano, PyMOL was initially commercialized by DeLano Scientific LLC, but is currently marketed by Schrödinger LLC. For more details, please either consult the Home page of incentive PyMOL by SCHRÖDINGER or the Home page of the open source project on GitHub.

Usage of PyMOL at LRZ

The environment modules package controls access to the software. Use "module avail pymol" to find all available versions of PyMOL installed at LRZ.

To use the default version of PyMOL, please type:

> module load pymol

Visualization using the PyMOL GUI

You can start the PyMOL GUI either on the login nodes of Linux-Cluster & SuperMUC-NG or by using our remote visualization service (via VNC). We however want to note that the graphics performance on the login nodes is comparatively poor. Therefore, we recommend our users to only start the PyMOL GUI on the login nodes for less demanding visualisations of e.g. small molecules, but not for CPU-intensive renderings using "ray". If you however either want to visualize larger data sets or perform CPU-intensive renderings using "ray", we recommend using our remote visualization service (via VNC) instead. You will then entirely have access to the reserved "localhost" node including GPU resources and can run CPU-intensive tasks within the PyMOL GUI.

To start PyMOL graphical user interface, simply type:

> pymol

Running PyMOL on the command line (for productive-level, publication-ready renderings)

Given the fact that rendering of 3D molecular structures can be very CPU-intensive tasks, we recommend our users to run PyMOL via the command line (salloc/srun or sbatch) on a whole node of either Linux Cluster or SuperMuc-NG to prepare high-quality, publication-ready molecular images.

For this purpose, you need a previously generated (using the PyMOL GUI either as shown above or on your local computer) ".pse" file containing both 3D coordinates of the molecular structures and information on how the structures should be visualized (e.g. cartoon or ball-and-stick representation).

Furthermore, you need a ".pml" file containing the rendering options:

load PSE_FILE_NAME.pse

Via an interactive SLURM shell (recommended for a few jobs or testing purposes)

To e.g. request one node on mpp2 of the Linux Cluster for half an hour, please issue:

> salloc --nodes=1 --time=00:30:00 --partition=mpp2_inter

For requesting one node on the test partition of SuperMuc-NG for half an hour, please issue:

> salloc --nodes=1 --time=00:30:00 --partition=test --account <project id>

When a new batch session is returned to you, simply type

> srun BINARY_NAME INPUT_FILE.inp

to run your SCHRÖDINGER application (for BINARY_NAME, please see the table above).

3.2.2. By submitting a SLURM batch script (recommended for production runs)

For production runs, please create a SLURM batch script and submit via sbatch.

#!/bin/bash
#SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
#SBATCH -e /dss/dsshome1/<group>/<user>/mydir/%x.%j.err #SBATCH -D /dss/dsshome1/<group>/<user>/mydir #SBATCH -J <job_name>
#SBATCH --time=24:00:00
#SBATCH --clusters=mpp2
#SBATCH --nodes=1 #SBATCH --export=NONE #SBATCH --get-user-env #SBATCH --mail-type=end #SBATCH --mail-user=<email_address>@<domain> source /etc/profile.d/modules.sh
module load schrodinger
BINARY_NAME INPUT_FILE.inp
#!/bin/bash
#SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
#SBATCH -e /dss/dsshome1/<group>/<user>/mydir/%x.%j.err
#SBATCH -D /dss/dsshome1/<group>/<user>/mydir
#SBATCH -J <job name>
#SBATCH --time=24:00:00
#SBATCH --partition=micro
#SBATCH --nodes=1
#SBATCH --export=NONE
#SBATCH --get-user-env
#SBATCH --mail-type=END
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --account=<project id>

module load slurm_setup
module load schrodinger

BINARY_NAME INPUT_FILE.inp

Documentation

Please consult the incentive PyMOL Home page for documentation. For PyMOL Command Reference, Quick Reference Guide for Intermediate PyMOL Users

Support

If you have any questions or problems with PyMOL installed at LRZ platforms, please don't hesitate to contact LRZ HPC support staff.

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