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PyMOL is a molecular visualization system. Please note that only the open-source version of PyMOL is available in the Department.

Instructions for users: 

On managed Linux workstations this is available as standard, just type pymol. The system version is not compatible with Ananconda so if you use Anaconda be sure to unload it before starting pymol.

On managed Windows workstations you may need to install the package via WPKG. If you are the registered user of the machine you want the package installing on, or are the group computer rep, you can select it for installation automatically at https://apps.ch.cam.ac.uk/wpkg/ .

The program may very well segfault on startup if it doesn't like your computer's video drivers. If this happens please get in touch with support@ch.cam.ac.uk to see what can be done about it (or use different visualisation software!)

Licence Details: 

/usr/local/shared/pymol/LICENSE on the workstations

Documentation: 

Unlike the program code, the documentation is not free. However there's quite a lot of stuff on the pymol wiki that might help.

Admin notes: 

Part of the distro on Ubuntu

To build needs libpng, freeglut, freetype2, python-tk. Also Python MegaWidgets, which is one of those things that installs OK with python setup.py install --prefix=/whatever.

There are binaries available for pymol but under restrictive licences so we compile from source on SuSE. The installation instructions I used were those found on the Pymol wiki at https://pymolwiki.org/index.php/Linux_Install. I put the 'pymol' script in the python bin directory.

Did separate versions for 32-bit and 64-bit image as they go into the local python directories and contain ELF binaries.

pymol is very picky about video drivers. It segfaults with the SuSE 11.1 'nv' driver. You can get round this by installing the driver from nvidia but I imagine there are other drivers it could have a problem with.

To test it I usually just run some examples off the wiki. At the time of writing there is a tutorial at https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners that suffices.

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