Linux Install

Installing PyMol is quite straightforward.

PyMol

Installing PyMol is very simple, even from source. On Linux, you need the following requirements:

• Python (with distutils)
• Pmw (Python Megawidgets)
• OpenGL driver (I use NVidia)

Generic Linux

From Source

• untar the compressed package;
• cd into the newly untarred directory (should be pymol or pymol-version).
• execute

  python setup.py install            # you may need to be root
  

• execute

  python setup2.py install           # you may need to be root
  

• execute

  cp ./pymol.com SOME_PATH           # where SOME_PATH is some directory in your $PATH
  

The executable name is "pymol.com".

From Package

Download the appropriate RPM and use 'rpm' to install it. Typically,

rpm -Uvh rpmFileName.rpm

Compiling By Hand

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

Fedora Core Linux (x86)

PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [1]

Alternatively, PyMOL can be installed using Yum (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray

And then issuing the following command as root:

yum install pymol

Gentoo Linux (x86)

as root:

emerge pymol

be sure to have the proper OpenGL configuration. For example:

opengl-update ati
opengl-update nvidia

list of available versions of pymol for gentoo

SuSe

32-bit (x86)

See [#Generic Linux] above.

64-bit (x86_64)

See [#Generic Linux] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol

• Ensure your system has it's distutils in place and ready to use. Try the following check:

from distutils import *

• Download the source
• Download [Pmw] from [SourceForge].
  • To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:

import * from Pmw

If errors erupt, investigate.

• decompress the source and cd into the PyMol directory that was just decompressed.
• If upgrading see below.
• Now enter the following...

python setup.py build
sudo python setup.py install
sudo python setup2.py

• The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path: sudo cp ./pymol.com /usr/local/bin

You should now have a working PyMol install.

pymol.com should now run your new PyMol install.

Preparing your System

See Linux_XFree86_Configuration.

Graphics

XFree86 Config

Check out Configuring XFree86 if you need information on editing the XFree86 configuration file.