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Installing PyMol is quite straightforward.
This page describes how to install PyMOL on Linux.


=PyMol=
== Incentive PyMOL ==
Installing PyMol is very simple, even from source.  On Linux, you need the following requirements:
* [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
 
== Generic Linux ==


=== Quick Install for Latest Features ===
[http://www.schrodinger.com Schrödinger] provides pre-compiled (64 bit) PyMOL to paying sponsors. The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG encoder for movie export, and a small molecule energy minimization engine.
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.


This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access.  It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it.  This should install PyMOL onto your system so that any users on your system can use it.  To easily get the latest version, do the following:
Download: https://pymol.org/
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.


== 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.


=== From Source ===
Command line install examples for some popular distributions (note that all of these commands must be run as root or superuser):
* Assuming that you're running under Linux, you'll need the following dependencies installed first:
python-devel, libpng-devel,
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install            # you may need to be root</source>
* execute <source lang="python">python setup2.py install          # you may need to be root</source>
* execute <source lang="python">cp ./pymol SOME_PATH          # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol".


=== From Package ===
<source lang="bash">
Download the appropriate RPM and use 'rpm' to install it.  Typically,
# Arch/Manjaro
rpm -Uvh rpmFileName.rpm
pacman -S pymol


===Compiling By Hand===
# CentOS with EPEL
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues.  To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.  The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
rpm -i http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-5.noarch.rpm
* tcl-8_4_11.tgz                       
yum --enablerepo=epel install pymol
* tk-8_4_11.tgz                       
* zlib-1_2_3.tgz                       
* libpng-1_2_8.tgz                     
* python-2_4_2.tgz                     
* numeric-24_2.tgz                     
* pmw-1_2.tgz                         
* freetype-2_1_10.tgz                 
--and--                                 
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)


====Supported Packages====
# Debian/Ubuntu/Mint
The above packages don't need to be installed from their source-packages only.  That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages.  '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages.  PyMOL needs the source/header files to compile against.  For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.
apt-get install pymol


   
# Fedora
dnf install pymol


Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.
# Gentoo
emerge -av pymol


Here's the basic steps to install by source:
# openSUSE (12.1 and later)
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
zypper install pymol
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com  # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make        # make appropriate changes
# vi setup.py          # make appropriate changes
# make


Warnings:
# Sabayon
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
equo i -av pymol
* ensure you have the correct Python path and version (is it 2.3?  2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
  LIBP=          $(exec_installdir)/lib'''''64'''''/python$(VERSION)
 
Copy the appropriate setup/Rules.XXX file to the base PyMol dir.  You'll have to edit the file for your system.  Then run 'make'.
 
==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL.  Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>
</source>


==== Installing a Script Without Superuser Access ====
== Install from source ==
Install the script following the instructions by the distributor.  Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).


== Fedora Core Linux (x86) ==
Installation from source gives you the latest version and is the generic way to install PyMOL.
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]


Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:
Please also consult the [https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL INSTALL] file.


[xray]
=== Requirements ===
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray


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


you may also need to add the pgp key for the repository before yum will get packages from it by either saying:
* C++11 compiler (e.g. GCC 4.7 or higher)
* [http://www.python.org/ Python] 3.6+
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* GLEW
* libpng
* freetype
* libxml2 (optional, for COLLADA export, disable with <code>--no-libxml</code>)
* [https://github.com/msgpack/msgpack-c msgpack-c] 2.1.5+ (optional, for fast [http://mmtf.rcsb.org/ MMTF] loading, new in SVN r4167, disable with <code>--use-msgpackc=no</code>)
* PyQt5, PyQt4, or PySide (optional, will fall back to Tk interface if compiled with <code>--glut</code>)
* [https://glm.g-truc.net/ glm]
* [https://github.com/rcsb/mmtf-cpp mmtf-cpp] (optional, for [http://mmtf.rcsb.org/ MMTF] export, disable with <code>--use-msgpackc=no</code>)
* libnetcdf (optional, disable with <code>--no-vmd-plugins</code>)


rpm --import http://www.bioxray.dk/~mok/404825e7.asc
Optional/deprecated:


or with older versions of rpm:
* [https://github.com/schrodinger/pmw-patched Pmw] (Python Megawidgets, for legacy GUI/plugins)
* GLUT/freeglut (enable with <code>--glut</code>)


wget http://www.bioxray.dk/~mok/404825e7.asc
On many Linux systems, one of the following commands installs all requirements (and must be run as root):
rpm --import 404825e7.asc


<source lang="bash">
# Debian/Ubuntu/Mint
apt-get install git build-essential python3-dev libglew-dev \
  libpng-dev libfreetype6-dev libxml2-dev \
  libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev


And then issuing the following command as root:
# CentOS
yum install gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel \
  msgpack-devel netcdf-devel


yum install pymol
# Fedora
dnf install gcc gcc-c++ kernel-devel python3-devel glew-devel PyQt5 msgpack-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel


== Gentoo Linux (x86) ==
# Gentoo
as root:
emerge -av dev-lang/python dev-python/pmw media-libs/glew \
emerge pymol
  media-libs/freeglut media-libs/libpng media-libs/freetype media-libs/glm
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]


A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
# openSUSE
layman -a dberkholz && emerge =sci-chemistry/pymol-9999
zypper install python-devel freeglut-devel gcc-c++ glew-devel libpng-devel python-pmw glm


There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
# Sabayon
svn co http://svn.olausson.de/molmod/trunk
equo i -av dev-lang/python dev-python/pmw media-libs/glew \
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.
  media-libs/freeglut media-libs/libpng media-libs/freetype
</source>


All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.
=== Get latest source from Git ===


== SuSe ==
<source lang="bash">
=== 32-bit (x86) ===
git clone https://github.com/schrodinger/pymol-open-source.git
See [[#Generic Linux]] above.
git clone https://github.com/rcsb/mmtf-cpp.git
 
mv mmtf-cpp/include/mmtf* pymol-open-source/include/
=== 64-bit (x86_64) ===
cd pymol-open-source
See [[#Generic Linux]] above. Some details for problem solving are here.  64-bit Python install is quite easy.  Make sure your nvidia driver is installed (or ATI, but I have no experience there).
 
To install PyMol
*Ensure your system has it's distutils in place and ready to use.  Try the following check:
<source lang="python">
from distutils import *
</source>
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/.  You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build<br>
sudo python setup.py install<br>
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.


I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
''The master branch requires Python 3.6+. Use the legacy [https://github.com/schrodinger/pymol-open-source/tree/py2 py2] branch for Python 2.7 compatibility.''
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''.  So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>


=== Libraries in non-standard places ===


You should now have a working PyMol install.
Optional: You may use the colon-delimited <code>$PREFIX_PATH</code> variable to point <code>setup.py</code> to non-standard locations of libraries and headers (those locations should have <code>include</code> and <code>lib</code> directories).


'''pymol.com''' should now run your new PyMol install.
=== Compile and install ===


==Ubuntu Linux (x86 32,64; mac ppc)==
This will install PyMOL as normal user into <code>$HOME/pymol-open-source-build</code>.


http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png
<source lang="bash">
#!/bin/bash -e


The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command
prefix=$HOME/pymol-open-source-build


sudo apt-get install pymol
# Example for dependencies in non-standard places
# export PREFIX_PATH="$HOME/extra/glew-2.0.0:$HOME/extra/libpng-1.6.5:/opt/local"


once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated. 
python3 setup.py build install \
    --home=$prefix
</source>


[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.
Now launch PyMOL like this:


'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.
<source lang="bash">
$HOME/pymol-open-source-build/bin/pymol
</source>


=Preparing your System=
=== Troubleshooting ===
See [[Linux_XFree86_Configuration]].


==Graphics==
* Do do a "clean" build, remove the "build" directory (sometimes necessary if "git pull" changed header files)
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.


[[Category:Installation|Linux Installation]]
* 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]


===Xorg===
== Customized Installations ==
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):


ModeLine    "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync
* [[User:Tlinnet/Linux_Install|Troels Linnet's installations scripts]]: Detailed installation scripts for Ubuntu, Mint 12 and RHEL 6, including MPEG support from FREEMOL


appears to slightly improve the stereo quality, in particular when one
[[Category:Installation|Linux Installation]]
displays labels and/or dashes/dots.
 
For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]
 
===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:
 
<pre>
Driver "nvidia"
</pre>
 
Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.
 
<pre>
Section "Extensions"
    Option "Composite" "Disable"
EndSection
</pre>
 
In Section "Screen" add the following line to enable quad-buffered stereo:
 
<pre>Option "Stereo" "3"</pre>
 
=Problems=
 
==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running.  Such examples could be SCIM, KINPUT/2 or the like.  Try turning off the IME and restarting PyMol to get the widgets to recognize your input.
 
==libnvidia-tls.so.1: cannot handle TLS data==
 
If you get an error, upon invoking pymol, of the form
 
<pre>
Traceback (most recent call last):
  File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
    import pymol
  File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
    import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>
 
then try changing the permissons on  libnvidia-tls.so.1.  i.e,
 
<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1  </pre>
 
==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL.  ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a
 
# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Latest revision as of 04:48, 5 June 2020

This page describes how to install PyMOL on Linux.

Incentive PyMOL

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.

Download: https://pymol.org/

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.

Please also consult the INSTALL file.

Requirements

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

  • C++11 compiler (e.g. GCC 4.7 or higher)
  • Python 3.6+
  • OpenGL driver (I use NVidia)
  • GLEW
  • libpng
  • freetype
  • libxml2 (optional, for COLLADA export, disable with --no-libxml)
  • msgpack-c 2.1.5+ (optional, for fast MMTF loading, new in SVN r4167, disable with --use-msgpackc=no)
  • PyQt5, PyQt4, or PySide (optional, will fall back to Tk interface if compiled with --glut)
  • glm
  • mmtf-cpp (optional, for MMTF export, disable with --use-msgpackc=no)
  • libnetcdf (optional, disable with --no-vmd-plugins)

Optional/deprecated:

  • Pmw (Python Megawidgets, for legacy GUI/plugins)
  • GLUT/freeglut (enable with --glut)

On many Linux systems, one of the following commands installs all requirements (and must be run as root): 

# Debian/Ubuntu/Mint
apt-get install git build-essential python3-dev libglew-dev \
  libpng-dev libfreetype6-dev libxml2-dev \
  libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev

# CentOS
yum install gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel \
  msgpack-devel netcdf-devel

# Fedora
dnf install gcc gcc-c++ kernel-devel python3-devel glew-devel PyQt5 msgpack-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel

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

# openSUSE
zypper install python-devel freeglut-devel gcc-c++ glew-devel libpng-devel python-pmw glm

# Sabayon
equo i -av dev-lang/python dev-python/pmw media-libs/glew \
  media-libs/freeglut media-libs/libpng media-libs/freetype

Get latest source from Git

git clone https://github.com/schrodinger/pymol-open-source.git
git clone https://github.com/rcsb/mmtf-cpp.git
mv mmtf-cpp/include/mmtf* pymol-open-source/include/
cd pymol-open-source

The master branch requires Python 3.6+. Use the legacy py2 branch for Python 2.7 compatibility.

Libraries in non-standard places

Optional: You may use the colon-delimited $PREFIX_PATH variable to point setup.py to non-standard locations of libraries and headers (those locations should have include and lib directories).

Compile and install

This will install PyMOL as normal user into $HOME/pymol-open-source-build. 

#!/bin/bash -e

prefix=$HOME/pymol-open-source-build

# Example for dependencies in non-standard places
# export PREFIX_PATH="$HOME/extra/glew-2.0.0:$HOME/extra/libpng-1.6.5:/opt/local"

python3 setup.py build install \
    --home=$prefix

Now launch PyMOL like this: 

$HOME/pymol-open-source-build/bin/pymol

Troubleshooting

  • Do do a "clean" build, remove the "build" directory (sometimes necessary if "git pull" changed header files)
  • 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

Retrieved from "https://pymolwiki.org/index.php?title=Linux_Install&oldid=13303"