PUPIL 2.0 Tutorial I: How to launch PUPIL 2.0 GUI

Step One: Setup your environmental variables.

I guesstimate most group members log into HPC with bash shell so I just use .bashrc and .bash_profile as examples. Actually you have two possible ways to setup your environmental variables for the sake of running PUPIL 2.0 and here they are.

Method I

Adding following statements into your .bashrc file:

# PUPIL 2.0
export PUPIL_PATH=/apps/shared/merz/pupil-2.0
export PATH=$PATH:/apps/shared/merz/pupil-2.0/bin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}\:${PUPIL_PATH}/lib

Method II (recommended)

Adding following statements into your .bash_profile file first:

#Check .bashrc file
test -r ${HOME}/.bashrc && . ${HOME}/.bashrc

# User specific environment and startup programs

for dir in ${PUPIL_PATH}/bin

do
case :${PATH}: in
:: ) PATH=${dir} ;;
*:${dir}:*) ;;
*) PATH=${dir}:${PATH} ;;
esac
done
export PATH

Then modifying your .bashrc file with:

# PUPIL 2.0
export PUPIL_PATH=/apps/shared/merz/pupil-2.0
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}\:${PUPIL_PATH}/lib

Step Two: Log into HPC test node.

[fu@submit2 ~]$ ssh -Y test05
Last login: Fri Mar 2 10:58:10 2012 from r11a-s18.ufhpc

Note: Seems like right now only test05 node has enough memory to run JAVA virtual machine. I do not know what happened on other test nodes and maybe I should sent an email to bugzilla. BTW, do not forget the -Y option for SSH command.

Step Three: Launch PUPIL 2.0 GUI.

[fu@r11a-s20 ~]$ pupil-gui



If you can see the above pic in your computer, congratulations! You got it!

(to be continued)

Exhibition of QM/MM Artwork

This figure exhibited a QM/MM refined anti-Alzheimer drug Aricept (orange ball-stick model) binding in its active site (PDB id 1EVE). After QM/MM X-ray refinement, few coordinate errors of this drug molecule were fixed which optimized its spatial orientation and facilitated the π- π interaction between ligand and three key binding residues (W84, W279 and F330). The electron density map was interpreted at σ = 1.5 contour level. The complex was rendered using PYMOL v1.2r1.

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