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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.


Situs User Guide