This is a read-only mirror of pymolwiki.org
Difference between revisions of "Linux Install"
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# Debian/Ubuntu/Mint | # Debian/Ubuntu/Mint | ||
| − | apt-get install build-essential | + | apt-get install git build-essential python3-dev libglew-dev \ |
| − | + | libpng-dev libfreetype6-dev libxml2-dev \ | |
| − | libmsgpack-dev | + | libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev |
# CentOS | # CentOS | ||
| Line 95: | Line 95: | ||
<source lang="bash"> | <source lang="bash"> | ||
git clone https://github.com/schrodinger/pymol-open-source.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 | cd pymol-open-source | ||
</source> | </source> | ||
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# export PREFIX_PATH="$HOME/extra/glew-2.0.0:$HOME/extra/libpng-1.6.5:/opt/local" | # export PREFIX_PATH="$HOME/extra/glew-2.0.0:$HOME/extra/libpng-1.6.5:/opt/local" | ||
| − | + | python3 setup.py build install \ | |
--home=$prefix | --home=$prefix | ||
</source> | </source> | ||
Revision as of 16:31, 10 January 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 (with distutils)
- Pmw (Python Megawidgets, optional, for legacy GUI/plugins)
- OpenGL driver (I use NVidia)
- GLEW
- GLUT/freeglut (optional, enable with
--glut) - 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)
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
# 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
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