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calcprop.pl
Usage
usage: calcprop.pl [options] tag
options: [-dir datadir]
[-natpdb file] [-chain id]
[-l min:max[=...]]
[PARALLELoptions]
Description
This script calculates (missing) structural properties for an ensemble.
It expects a tag as argument to identify a set of structures.
The option -dir is available to specify the directory
under which the ensemble is stored if it is not the current directory.
The calculation of most structural properties requires a reference
structure that can be supplied with -natpdb if none has
been given previously. Other options that can be set if necessary
include a fragment list with -l and a chain selection in multi-domain structures
with -chain.
Options
- -help
- usage information
Examples
calcprop.pl -natpdb 1vii.exp.pdb sample
calculates structural properties for the ensemble structures
associated with the sample tag under the current
directory. The native
reference structure is taken from 1vii.exp.pdb.
calcprop.pl -natpdb 1vii.exp.pdb -dir data -cpus 4 sample
calculates structural properties for the ensemble structures
associated with the sample tag under the
data directory. 4 threads are used to perform
the calculation in parallel. The native
reference structure is taken from 1vii.exp.pdb.
calcprop.pl -dir data -cpus 4 -hosts sgi.workstations sample
calculates ensemble properties in parallel on 4 cpus by remote
job submission to hosts from sgi.workstations.
calcprop.pl -dir data -cpus 4 -mp -hosts sgi.local sample
calculates ensemble properties in parallel on 4 cpus by remote
job submission to hosts from sgi.local. Local
directories are used on the client nodes as given in the host
file.