PyMOL is a molecular visualisation tool originally developed by Dr. Warren DeLano, who unfortunately passed away about one week ago. It is the most intuitive program of its kind I’ve used, it supports scripting with both its own “language” and Python, and best of all, it’s free and open-source. This is a small guide on how to install PyMOL on Ubuntu. It’s my own contribution to the effort of keeping PyMOL alive even after its founder’s death.
If you’re looking for a(n even) simple(r) method, just apt-get pymol:
sudo apt-get install pymol
If you want the last version though, which is likely NOT to be in the repositories, this is how you do it. Again, PyMOL Wiki has pretty much all the info you need, this is just my own recollection :)
The most recent version is usually the one you want to install and is only available through Subversion. To download it, you first need to install a Subversion client. The easiest is:
sudo apt-get install subversion
Then, you need to download PyMOL itself using this tool. It takes quite a bit (a couple of minutes). The following command will create a directory where it will download the software components needed for the installation. I’ll install mine on /home/joao/Software
cd /home/joao/Software svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
This will create a directory called pymol which has all the following structure:
joao@muse:~/Software$ ls pymol/ aclocal.m4 config.sub DEVELOPERS layer3 Makefile.delsci products acsite.m4 configure examples layer4 Makefile.in README AUTHORS configure.ac INSTALL layer5 missing scripts autogen.sh contrib install-sh LICENSE modules setup ChangeLog COPYING layer0 ltmain.sh NEWS setup2.py config.guess data layer1 m4 ov setup.py config.h.in depcomp layer2 Makefile.am PACKAGING test joao@muse:~/Software$
If you try to run the setup.py files, they will break because you are most likely missing dependencies. PyMOL needs the following packages to work properly:
python-dev ( will install python-dev and python obviously )
python-pmw ( will install tcl8.x and tk8.x as well, and these are also needed )
libpng-dev ( will install libpngxx and libpngxx-dev )
freeglut-dev ( will install freeglutx-dev and freeglutx, as well as a bunch of other packages )
libfreetypeX-dev ( will install libfreetypeX and libfreetypeX-dev )
And also, if you’re in a clean, pure, freshly installed system you’ll need the usual bunch: sudo apt-get install build-essential
After these are solved, you can proceed to actually install PyMOL. First, you have to know if you want to install it system-wide (you’ll need root privileges for this) or locally ( in a place like your home directory, which is our case ). Local installtion is easier to maintain in my opinion, and you always have permissions for it so that’s the one I’ll explain.
Enter the pymol directory and run this command:
python setup.py install --prefix /path/to/install/directory
The part in bold is where you define the location of the installation directory. So, in my case, I want my PyMOL to be installed in /home/joao/Software/pymol I put this in front of the –prefix.
After the building is completed, you’ll have to do one thing extra ( and not mentioned in the final output of setup.py ):
This basically tells the next script, setup2.py, where to find the pymol libraries/modules/whatever it needs to install. In my example, they are in the pymol directory ( the one I chose in the prefix ). So, my command looks like:
Then, the second script can be called:
python setup2.py install --prefix /home/joao/Software/pymol
This will create a pymol executable in the directory you chose. You can then link this executable to make it available easily with:
sudo ln -s /home/joao/Software/pymol/pymol /usr/bin
And now, running pymol in your command line should launch PyMOL smoothly! Easy :) This approach also has the advantage of updating your pymol super easily:
If you do the previous in your pymol directory it will fetch the latest versions of each file. I “think” (I’m not sure) that this will not need another installation round, but in any case, it’s easy enough.
That’s it, your ready to use PyMOL to create lovely pictures and check your molecules! Check here for tutorials. And if you’re in a generous mood, consider donating to the Warren DeLano Memorial Fund. It will help keep open-source initiatives such as PyMOL alive.