Tool Set Documentation

Revision as of 14:18, 12 August 2006 by Feig (talk | contribs)
(diff) ←Older revision | view current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search


usage: [options] [seqFile chainFile | pdbFile]
options: [-par stiff=val,short=val,central=val,kdcore=val,

Show source


This script can be used to evaluate the SICHO energy function for a given lattice chain without actually running MONSSTER. The input can be either a sequence and chain file in MONSSTER format or a chain PDB file that can be generated with <docmark></docmark>.
Scaling factors for various energy components in the SICHO energy function can be specified with -par followed by key=value pairs. A more detailed explanation can be found in the description of <docmark></docmark>.
The output consists of the total energy, as well as the individual energy components for short-range interactions, pair-wise interactions, a burial term, a burial correction term, and a centrosymmetric term.


usage information

Examples 1vii.seq 1vii.exp.chain
evaluates the SICHO energy of the given input chain

78.964588 31.031346 46.683241 -0.600000 6.900000 -5.050000 -par central=0.5,pair=2.0 1vii.seq 1vii.exp.chain
evaluates the SICHO energy function with different scaling factors

72.252088 31.031346 38.720741 -0.600000 6.900000 -3.800000