Linux Install: Difference between revisions
Line 22: | Line 22: | ||
===Compiling By Hand=== | ===Compiling By Hand=== | ||
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. Here's | 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. | ||
Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''. | |||
Here's the basic steps to install by source: | |||
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source] | # get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source] | ||
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory | # extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory |
Revision as of 08:54, 11 January 2006
Installing PyMol is quite straightforward.
PyMol
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
Generic Linux
From Source
- untar the compressed package;
- cd into the newly untarred directory (should be pymol or pymol-version).
- execute
python setup.py install # you may need to be root
- execute
python setup2.py install # you may need to be root
- execute
cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH
The executable name is "pymol.com".
From Package
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm
Compiling By Hand
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.
Once downloaded, see the file pymol/INSTALL and pymol/INSTALL.generic.
Here's the basic steps to install by source:
- get the source PyMol Source
- 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:
- if you're using a 64-bit machine, lib becomes lib64 for almost everything
- 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.
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'.
Fedora Core Linux (x86)
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [1]
Alternatively, PyMOL can be installed using 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:
[xray] name=MOKs RPM Repository fedora $releasever - $basearch - xray baseurl=http://apt.bioxray.dk/fedora/$releasever/$basearch/xray
And then issuing the following command as root:
yum install pymol
Gentoo Linux (x86)
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati opengl-update nvidia
list of available versions of pymol for gentoo
SuSe
32-bit (x86)
See [#Generic Linux] above.
64-bit (x86_64)
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:
from distutils import *
- Download the source
- Download [Pmw] from [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:
import * from Pmw
If errors erupt, investigate.
- decompress the source and cd into the PyMol directory that was just decompressed.
- If upgrading see below.
- Now enter the following...
python setup.py build
sudo python setup.py install
sudo python setup2.py
- 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:
sudo cp ./pymol.com /usr/local/bin
You should now have a working PyMol install.
pymol.com should now run your new PyMol install.
Preparing your System
See Linux_XFree86_Configuration.
Graphics
XFree86 Config
Check out Configuring XFree86 if you need information on editing the XFree86 configuration file.