Difference between revisions of "Linux Install"

Revision as of 16:39, 2 June 2015

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
libxml2

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"

# Note this last command may need to be run as root, such as by adding 'sudo' before it
python setup.py build install \
    --home=$prefix \
    --install-lib=$modules \
    --install-scripts=$prefix

Now launch PyMOL like this:

/opt/pymol-svn/pymol

Optionally, in order to allow running the command pymol from the terminal to launch the program do:

ln -s /opt/pymol-svn/pymol /usr/bin/pymol

Updating

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.

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.

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

Customized Installations

Troels Linnet's installations scripts: Detailed installation scripts for Ubuntu, Mint 12 and RHEL 6, including MPEG support from FREEMOL

@@ Line 84: / Line 84: @@
 export CPPFLAGS="-std=c++0x"
+# Note this last command may need to be run as root, such as by adding 'sudo' before it
 python setup.py build install \
      --home=$prefix \
@@ Line 90: / Line 91: @@
 </source>
-Now launch PyMOL like this (you may copy this launcher into your '''$PATH''',
+Now launch PyMOL like this:
-like to '''/usr/local/bin'''):
 <source lang="bash">
@@ Line 99: / Line 99: @@
 Optionally, in order to allow running the command <code>pymol</code> from the terminal to launch the program do:
 <source lang = "bash">
-ln -s /opt/pymol-svn/pymol /usr/local/bin/pymol
+ln -s /opt/pymol-svn/pymol /usr/bin/pymol
 </source>
@@ Line 106: / Line 106: @@
 <source lang = "bash">
 sudo rm -r /opt/pymol-svn/pymol
+rm -r /tmp/pymol
 </source>
 and redo the installation from the beginning with the latest release.