MMTSB
Tool Set Documentation

calcprop.pl

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Usage

usage:   calcprop.pl [options] tag
options: [-dir datadir]
         [-natpdb file] [-chain id]
         [-l min:max[=...]]
         [PARALLELoptions]
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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.

Only missing properties are computed, values that have been computed before are not overwritten. For large ensembles the calculation of structural properties may take a while to complete. Several options are available to speed up the calculation by running in parallel depending on available architectures. The list of options can be found here. Ensemble properties can also be set from external data with setprop.pl. Ensemble properties may be queried with getprop.pl.

Options

-help 
usage information
-dir directory 
data directory
-natpdb file 
provide reference structure
-chain id 
indicate which chain to compare to in reference
-l min:max[=...] 
limit RMSD comparison to specified residue range

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.