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.
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)
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 libxml2-dev # Fedora/CentOS yum install subversion gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \ freeglut-devel libpng-devel freetype-devel libxml2-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 # enable c++11 export CPPFLAGS="-std=c++0x" # If you want to install as root, then split this line up in "build" # and "install" and run the "install" with "sudo" python setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix
Now launch PyMOL like this:
Optionally, in order to allow running the command
pymol from the terminal to launch the program do:
sudo ln -s /opt/pymol-svn/pymol /usr/bin/pymol
To update the installation merely run:
sudo rm -r /opt/pymol-svn/pymol rm -r /tmp/pymol
and redo the installation from the beginning with the latest release.
- 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-pmwto 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.
- 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 Ubuntu community Nvidia Drivers How To
- Troels Linnet's installations scripts: Detailed installation scripts for Ubuntu, Mint 12 and RHEL 6, including MPEG support from FREEMOL