Linux Install

Installing PyMol is quite straightforward.

XFree86 Config

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

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:

http://apt.bioxray.dk/

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

64-bit (x86_64)

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.

• Caveats
  • NVidia card
    • Kernel Source
  • ATI card
  • Pmw

RPM

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

rpm -Uvh rpmFileName.rpm

From Source

DistUtils

assuming you already have your PyMol source tree untar'ed simply do:

 python setup.py build
 python setup.py install  # need to be root, here
 python setup2.py 
 sudo cp ./pymol.com /usr/local/bin/pymol.com # cp the executable to /usr/local/bin

Now you can run PyMol from anywhere by issuing the command:

pymol.com

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'.

Preparing your System

See Linux_XFree86_Configuration.