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Situs on Biowulf

Situs is a package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

Situs website

Situs is a single-threaded application and cannot use multiple processors on a node.

Situs is installed in /usr/local/situs. The paths can be set up correctly by using the 'module load situs' command.

Sample Situs job

Create a batch script containing the Situs commands, along the following lines:

--------- /data/username/myrun ------------
#!/bin/bash -v
#PBS -N Situs
#PBS -m be
#PBS -k oe

module load situs
cd /data/username/situs
map2map 0_mt.ascii 1_mt.situs
voldiff 1_nm.situs 1_mt.situs 2_s1.situs
volhist 3_nm.situs test
qrange 4_s1.situs 0_ncd.pdb
---------------- end of script -------------

Submit this job with qsub:

qsub -l nodes=1 myrun

Examination of structures via VMD is best performed on Helix, which is intended for interactive use. Open an Xwindows session to Helix and start up VMD.

Documentation

Situs User Guide