PyMOL
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.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of pymol and load default version of pymol as
module avail pymol/ # list available modules module load pymol # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail pymol
and choose explicit version you want to use. Load and run example:
module add pymol-2.3.4 # or (for using older version) module add pymol-1.8.2.1-gcc debian8-compat
# running the app pymol
Pymol command will open a graphical window.
Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.
Notice: Versions 1.8.2.1, 1.7.6 were compiled with Python 2, so it can be used with Python 2.
Documentation
Documentation is available at http://www.pymolwiki.org/index.php/Main_Page or https://pymol.org.