This page describes how to install PyMOL on Linux.
Schrödinger provides pre-compiled (64 bit) PyMOL to paying sponsors. The bundle also includes ready-to-use APBS, RigiMOL, an MPEG encoder for movie export, and a small molecule energy minimization engine.
Open-Source PyMOL in Linux Distros
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 (note that all of these commands must be run as root or superuser):
# Arch/Manjaro pacman -S 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 # Debian/Ubuntu/Mint apt-get install pymol # Fedora dnf install pymol # Gentoo emerge -av pymol # openSUSE (12.1 and later) zypper install pymol # Sabayon equo i -av 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 (and must be run as root):
# Debian/Ubuntu/Mint apt-get install subversion build-essential python-dev python-pmw libglew-dev \ freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev # CentOS yum install subversion gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \ freeglut-devel libpng-devel freetype-devel libxml2-devel # Fedora dnf 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 zypper install python-devel freeglut-devel gcc-c++ glew-devel libpng-devel python-pmw subversion # Sabayon equo i -av dev-vcs/subversion dev-lang/python dev-python/pmw media-libs/glew \ media-libs/freeglut media-libs/libpng media-libs/freetype
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
Troubleshooting: Connection refused...
If the above address is not available, giving an error such as
Connection refused: Unable to connect to a repository at URL 'svn://svn.code.sf.net/p/pymol/code/trunk/pymol': Can't connect to host 'svn.code.sf.net': Connection refused...
you can try using
http:// instead of
svn:// in the URL.
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