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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 consult either consult the Home page of incentive PyMOL by SCHRÖDINGER or the Home page of the open source project on GitHub.

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Usage of PyMOL at LRZ

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To use the default version of PyMOL, please type:

> module load pymol

Visualization using the PyMOL GUI

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To start PyMOL graphical user interface, simply type:

> pymol

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

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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 at least the "load" command to import the ".pse" file, the rendering options:

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"ray" command with the number of pixels in width and hight to render/raytrace the molecular structures and the "png" command to save the rendered scene in a ".png" file. Furthermore, the ".pml" file can contain additional rendering commands (e.g., set_view ..., space rgb/cmyk, hide ..., set ...) that at least in part could have been applied at the time the ".pse" file has been generated.

Code Block
languagetext
load PSE_FILE_NAME.pse
ray 2000, 1500
png PNG_FILE_NAME.png

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

pymol -c PML_FILE_NAME

INPUT_FILE

.

inp

pml

to run your SCHRÖDINGER application (for BINARY_NAME, please see the table above)save the rendered/raytraced scence in a ".png" file.

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
pymol

BINARY_NAME INPUT
pymol -c PML_FILE_NAME.
inp
pml
#!/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

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pymol

pymol -c PML_FILE_NAME.pml

Documentation

For documentation, please consult the incentive PyMOL Home page for documentation. For , the PyMOL Command Reference, or the 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.