Linux Install

2013-10-11T15:16:46Z

LunaDeferrari:

This page describes how to install open-source PyMOL on Linux.

== Install distribution specific binary package ==

Many Linux distributions provide binary packages for open-source PyMOL. They often do not provide the latest version, but if the provided package fits your needs this is the most convenient way to install PyMOL.

Command line install examples for some popular distributions:

<source lang="bash">
# Debian/Ubuntu/Mint
sudo apt-get install pymol

# Fedora
yum install pymol

# Gentoo
emerge -av pymol

# openSUSE (12.1 and later)
sudo zypper install pymol

# CentOS with EPEL
rpm -i http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-5.noarch.rpm
yum --enablerepo=epel install pymol
</source>

== Install from source ==

Installation from source gives you the latest version and is the generic way to install PyMOL.

=== Requirements ===

Libraries as well as development files (headers) of the following software is
required:

* [http://subversion.apache.org/ Subversion] to download the source code
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng
* freetype

On many Linux systems, one of the following commands installs all requirements:

<source lang="bash">
# Debian/Ubuntu/Mint
sudo apt-get install subversion build-essential python-dev python-pmw libglew-dev freeglut3-dev libpng-dev libfreetype6-dev

# Fedora/CentOS
yum install subversion yum install gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel freeglut-devel libpng-devel freetype-devel

# Gentoo
emerge -av dev-vcs/subversion dev-lang/python dev-python/pmw media-libs/glew \
media-libs/freeglut media-libs/libpng media-libs/freetype

# openSUSE
sudo zypper install python-devel freeglut-devel gcc-c++ glew-devel libpng-devel python-pmw subversion
</source>

=== Get latest source from SVN ===

This will download the latest source to '''/tmp/pymol''':

<source lang="bash">
cd /tmp
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
cd pymol
</source>

=== Compile and install ===

This will install PyMOL as normal user into '''/opt/pymol-svn'''. If you don't have write permissions to '''/opt''', change the <code>prefix</code> variable to something like '''$HOME/pymol-svn'''.

<source lang="bash">
#!/bin/bash -e

prefix=/opt/pymol-svn
modules=$prefix/modules

python setup.py build install \
--home=$prefix \
--install-lib=$modules \
--install-scripts=$prefix
</source>

Now launch PyMOL like this (you may copy this launcher into your '''$PATH''',
like to '''/usr/local/bin'''):

<source lang="bash">
/opt/pymol-svn/pymol
</source>

=== Troubleshooting ===

* On Linux Mint 11 there have been reports of gcc-4.5 breaking Pymol. You could use gcc-4.4 instead. (reported by [[User:Tlinnet]])
<div style="margin-left: 2em;">
<source lang="bash">
sudo apt-get install build-essential gcc-4.4 g++-4.4
export CC=/usr/bin/gcc-4.4
</source>
</div>

* If you get an error message "ImportError: No module named Pmw" and lack half of the user interface, then append <code>--bundled-pmw</code> to the install command line.

* If you're using Ubuntu 11.10 with an Intel Sandy Bridge video card and get graphics oddities. Please see [https://launchpad.net/~glasen/+archive/intel-driver Intel Driver Post for Ubuntu].

* If you are using Ubuntu with a NVIDIA graphic card and generic drivers you may experience bad rendering, black pixelation and other graphical oddities. A guide to installing NVIDIA proprietary drivers can be found under [https://help.ubuntu.com/community/BinaryDriverHowto/Nvidia Ubuntu community Nvidia Drivers How To]

== Customized Installations ==

* [[User:Tlinnet/Linux_Install|Troels Linnet's installations scripts]]: Detailed installation scripts for Ubuntu, Mint 12 and RHEL 6, including MPEG support from FREEMOL

[[Category:Installation|Linux Installation]]

PyMOL Wiki - User contributions [en]

Linux Install