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LSim: Input Command File

LSim is invocated trough a shell comand

lsim job.cmd

A command file job.cmd looks like:

/gscan /bpdb /verbose /nmax=10
1MBS.pdb
1SCT.pdb

The first line is the command line. The following lines are the PDB file entries, one per line. A blank line indicates the command file termination. A .cmd extension is always assumed.

LSim commands

/gscan
Scans Similarity function for a global maximization. When disabled a local maximization starts at LSim standard orientation.

/bpdb
Forces reading B temperature factors from PDB files. When disabled or when B is read as zero, the standard B factor from lsim.par is used instead.

/verbose
Extra printing.

/nmax or /nmax=n
Performs nmax local optimizations at the best scanned orientations. Note that higher nmax values enhance global optimization, though it increases the computational cost. Non-repeated multiple maxima are printed.

Additional LSim parameters are located at the lsim.par file. Their modification, however, is discouraged. The LSim parameters are:

vcut
Accuracy threshold for atom-atom similarity.

bfac
Standard B factors.

matdir
Number of director atoms in CAC global search.

maxiter
Maximum iterations.