I was searching in YouTube for a video and I got this error message:

Error 500 Internal Server Error

It was followed by a note stating that monkeys had been dispatched to take care of the problem and a bunch of characters likely describing the problem in monkey language. Well, the monkeys are probably GMT-based because my problem was not solved quickly. So I looked for a solution and came up with this:

Go to the bottom of the YouTube page. Change the language definition from yours (I had Portuguese) to another such as “English (UK)”. It worked wonders for me. Apparently the monkeys can’t speak/understand portuguese queries ;)

PyMOL is a molecular visualisation tool originally developed by Dr. Warren DeLano, which 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 ):

export PYTHONPATH=$PYTHONPATH:/path/to/install/lib/python{version}/site-packages

export PYTHONPATH=$PYTHONPATH:/home/joao/Software/pymol/lib/python2.6/site-packages/

python setup2.py install --prefix /home/joao/Software/pymol

sudo ln -s /home/joao/Software/pymol/pymol /usr/bin

svn up

Para mim, o guião devia ter sido sempre assim!

Dragon Ball…Our Herooooooooo!

enfim….

Uma boa razão para não se escrever no MSN e tentar trabalhar ao mesmo tempo :P

joao@muse:~/Desktop/Proposal/Modelling/C3$ eheh
eheh: command not found
joao@muse:~/Desktop/Proposal/Modelling/C3$