Pymol

Please note that this application page is referring to the old CentOS software stack which is obsolete and does not work any more with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page.

Category

Visualization, Python

Description

PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
	1.7.4, 1.8.4

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
1.7.4	module load gcc/4.8.2 python/2.7.6 pymol/1.7.4	openblas/0.2.13_seq
1.8.4	module load gcc/4.8.2 python/2.7.6 pymol/1.8.4	openblas/0.2.13_seq

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Interactive session

In order to start an interactive PyMOL session on one of the login nodes, you need to login to the Euler cluster with X11 forwarding enabled. Afterwards you can load the required modules and start PyMOL with the command pymol.

PyMOL GUI, please click on the picture to see a larger version

Example

As an example for using PyMOL, we will render a cartoon image of a protein (1bl8). If you would like to repeat the example, then please start an interactive PyMOL session on a login node and type the following sequence of commands in PyMOL

fetch 1bl8
show cartoon
hide lines, all
set depth_cue, 0
set spec_reflect, 0
set bg_rgb=[1,1,1]
set orthoscopic, on
set cartoon_fancy_helices, 1
set cartoon_smooth_loops, 1
set cartoon_highlight_color, 1
set ray_shadows, 0
set ray_texture, 1
ray

This is, what the result should then look like:

PyMOL example for rendering a protein. Please click on the picture to see a larger version

License information

BSD-style license

Links

https://www.pymol.org

https://pymolwiki.org/index.php/Main_Page