365. Compile firefox 19 on Debian Testing/Wheezy

There are issues with the official firefox binary since it's a 32 bit build and Wheezy isn't handling multiarch properly yet (plenty of conflicts between 32 and 64 bit packages)

So here's how to build a proper 64 bit firefox 19 on debian testing:

sudo apt-get install bzip2 build-essential python zip unzip pkg-config libgtk2.0-dev gconf2 libdbus-1-dev libdbus-glib-1-dev yasm libasound2-dev libcurl4-gnutls-dev libxt-dev mesa-common-dev
mkdir ~/tmp/firefox -p
cd ~/tmp/firefox
wget ftp://ftp.mozilla.org/pub/firefox/releases/19.0.2/source/firefox-19.0.2.source.tar.bz2
rm mozilla-release -rf
tar xvf firefox-19.0.2.source.tar.bz2
mkdir buildfirefox19/
cd buildfirefox19/
../mozilla-release/./configure --prefix=$HOME/.firefox19
make
make install
echo "alias firefox19='$HOME/.firefox19/bin/firefox'" >> $HOME/.bashrc
source $HOME/.bashrc

Start by running firefox19 from the terminal.

364. Setting up a new user on a ROCKS cluster

Because I keep forgetting about the rocks sync command...

From https://groups.google.com/forum/?fromgroups=#!topic/rocks-clusters/P6tvn_2Gk5Y

To add a new user to a ROCKS cluster and let them use Sun Grid Engine, do the following

sudo useradd -m verahill
sudo passwd verahill
su verahill
exit
sudo usermod -a -G compchem verahill
rocks sync users
qconf -auser verahill

      1 name verahill
      2 oticket 0
      3 fshare 0
      4 delete_time 0
      5 default_project NONE

where compchem is a usergroup I've set up to give everyone access to the executables they need.

The first login, using su above, creates the .ssh directory and rsa/dsa keys.

Finally, to force the user to change their password on first login, do

chage -d 0 verahill

363. Generating an image in PyMol

For some reason I needed to quickly generate a publication quality figure of a protein.

Deep View (SWiss PDB viewer) isn't available for linux anymore, and the old versions rely on 32 bit libs (which is increasingly a headache on debian). Rasmol is a classic, but I haven't used it properly since 1997 -- and all attempts at exporting png, jpg etc. failed on my debian wheezy box.

Jmol is awesome, and while I managed to make some pretty convincing figures I never quite got to where I wanted.

So I tried pymol

Pymol, like rasmol and jmol, has a visual interface which can be controlled via an integrated terminal. The learning curve is steep, but it's quick and easy to make figures once you've got the basics.

---

Install pymol from the repos in debian:
sudo apt-get install pymol

(on Archlinux you can get it via AUR  -- you'll need to install python-pmw first)

Download 1SU4.pdb from here http://www.rcsb.org/pdb/explore.do?structureId=1su4

In the directory where your pdb file is, do

pymol 1SU4.pdb

select helices, chain A

Click on the A(ction) by (helices), select preset/publication.

 select calcium, (res 995-996)
 show spheres, calcium

 Note that 'helices' and 'calcium' are just handles or aliases that I made up.

 alter calcium, vdw=5
 show spheres, calcium

 color purple calcium
 bg_color white

 set antialias=1
 set sphere_mode=5

where sphere_mode 5 means shading.

 ray 1000,1000

 save 1SU4.png

And here's the final figure: