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

Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the ext package and the PyMol source and compile/install by hand. Here's how

1. get the source PyMol Source
2. extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
3. cd pymol
4. cd ext
5. vi build.com # edit the build file
6. cd ..
7. cp setup/Rules.make . # or correct Rules.make file for your machine
8. vi Rules.make # make appropriate changes
9. vi setup.py # make appropriate changes
10. make

Warnings:

• if you're using a 64-bit machine, lib becomes lib64 for almost everything
• ensure you have the correct Python path and version (is it 2.3? 2.4?)
• make sure you make the changes in Rules.make, setup.py, and Makefile, for your platform.

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.