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| − | This page describes how to install | + | This page describes how to install PyMOL on Linux. |
| − | == | + | == Incentive PyMOL == |
| + | |||
| + | [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. | ||
| + | |||
| + | 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. | 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: | + | Command line install examples for some popular distributions (note that all of these commands must be run as root or superuser): |
<source lang="bash"> | <source lang="bash"> | ||
| + | # 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 | # Debian/Ubuntu/Mint | ||
| − | + | apt-get install pymol | |
# Fedora | # Fedora | ||
| − | + | dnf install pymol | |
# Gentoo | # Gentoo | ||
| Line 18: | Line 31: | ||
# openSUSE (12.1 and later) | # openSUSE (12.1 and later) | ||
| − | + | zypper install pymol | |
| − | # | + | # Sabayon |
| − | + | equo i -av pymol | |
| − | |||
</source> | </source> | ||
| Line 28: | Line 40: | ||
Installation from source gives you the latest version and is the generic way to install PyMOL. | Installation from source gives you the latest version and is the generic way to install PyMOL. | ||
| + | |||
| + | Please also consult the [https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL INSTALL] file. | ||
=== Requirements === | === Requirements === | ||
| Line 34: | Line 48: | ||
required: | required: | ||
| − | * | + | * C++11 compiler (e.g. GCC 4.7 or higher) |
| − | * [http://www.python.org/ Python] | + | * [http://www.python.org/ Python] 3.6+ |
| − | |||
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia]) | * OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia]) | ||
| + | * GLEW | ||
* libpng | * libpng | ||
* freetype | * freetype | ||
| − | * libxml2 | + | * 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>) | ||
| + | |||
| + | Optional/deprecated: | ||
| + | |||
| + | * [https://github.com/schrodinger/pmw-patched Pmw] (Python Megawidgets, for legacy GUI/plugins) | ||
| + | * GLUT/freeglut (enable with <code>--glut</code>) | ||
| − | On many Linux systems, one of the following commands installs all requirements: | + | On many Linux systems, one of the following commands installs all requirements (and must be run as root): |
<source lang="bash"> | <source lang="bash"> | ||
# Debian/Ubuntu/Mint | # 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 | + | # Fedora |
| − | + | dnf install gcc gcc-c++ kernel-devel python3-devel glew-devel PyQt5 msgpack-devel \ | |
| − | freeglut-devel libpng-devel freetype-devel libxml2-devel | + | freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel |
# Gentoo | # Gentoo | ||
| − | emerge -av | + | emerge -av dev-lang/python dev-python/pmw media-libs/glew \ |
| − | media-libs/freeglut media-libs/libpng media-libs/freetype | + | media-libs/freeglut media-libs/libpng media-libs/freetype media-libs/glm |
# openSUSE | # 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 | ||
</source> | </source> | ||
| − | === Get latest source from | + | === Get latest source from Git === |
| − | |||
| − | |||
<source lang="bash"> | <source lang="bash"> | ||
| − | + | git clone https://github.com/schrodinger/pymol-open-source.git | |
| − | + | git clone https://github.com/rcsb/mmtf-cpp.git | |
| − | cd pymol | + | mv mmtf-cpp/include/mmtf* pymol-open-source/include/ |
| + | cd pymol-open-source | ||
</source> | </source> | ||
| + | |||
| + | ''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.'' | ||
| + | |||
| + | === Libraries in non-standard places === | ||
| + | |||
| + | Optional: You may use the colon-delimited <code>$PREFIX_PATH</code> variable to point <code>setup.py</code> to non-standard locations of libraries and headers (those locations should have <code>include</code> and <code>lib</code> directories). | ||
=== Compile and install === | === Compile and install === | ||
| − | This will install PyMOL as normal user into | + | This will install PyMOL as normal user into <code>$HOME/pymol-open-source-build</code>. |
<source lang="bash"> | <source lang="bash"> | ||
#!/bin/bash -e | #!/bin/bash -e | ||
| − | prefix= | + | prefix=$HOME/pymol-open-source-build |
| − | + | ||
| + | # Example for dependencies in non-standard places | ||
| + | # export PREFIX_PATH="$HOME/extra/glew-2.0.0:$HOME/extra/libpng-1.6.5:/opt/local" | ||
| − | + | python3 setup.py build install \ | |
| − | --home | + | --home=$prefix |
| − | |||
| − | |||
</source> | </source> | ||
| − | Now launch PyMOL like this | + | Now launch PyMOL like this: |
| − | |||
<source lang="bash"> | <source lang="bash"> | ||
| − | + | $HOME/pymol-open-source-build/bin/pymol | |
</source> | </source> | ||
=== Troubleshooting === | === 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 [https://help.ubuntu.com/community/BinaryDriverHowto/Nvidia Ubuntu community Nvidia Drivers How To] | * 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] | ||
Latest revision as of 05:01, 22 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
- Troels Linnet's installations scripts: Detailed installation scripts for Ubuntu, Mint 12 and RHEL 6, including MPEG support from FREEMOL