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Linux Install
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:
# 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
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:
- Subversion to download the source code
- Python (with distutils)
- Pmw (Python Megawidgets)
- OpenGL driver (I use NVidia)
- libpng
- freetype
On many Linux systems, one of the following commands installs all requirements:
# 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
Get latest source from SVN
This will download the latest source to /tmp/pymol:
cd /tmp
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
cd pymol
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 prefix
variable to something like $HOME/pymol-svn.
#!/bin/bash -e
prefix=/opt/pymol-svn
modules=$prefix/modules
python setup.py build install \
--home=$prefix \
--install-lib=$modules \
--install-scripts=$prefix
Now launch PyMOL like this (you may copy this launcher into your $PATH, like to /usr/local/bin):
/opt/pymol-svn/pymol
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)
sudo apt-get install build-essential gcc-4.4 g++-4.4
export CC=/usr/bin/gcc-4.4
- If you get an error message "ImportError: No module named Pmw" and lack half of the user interface, then append
--bundled-pmw
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 Intel Driver Post for Ubuntu.
Customized Installations
- Troels Linnet's installations scripts: Detailed installation scripts for Ubuntu, Mint 12 and RHEL 6, including MPEG support from FREEMOL