Difference between revisions of "calcprop.pl"

Revision as of 18:50, 2 November 2006

Usage

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

Show source

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.

@@ Line 15: / Line 15: @@
 include a fragment list with <B>-l</B> and a chain selection in multi-domain structures
 with <B>-chain</B>.<BR>
-Only missing properties are computed, values that have been computed
-before are not overwritten.<BR>
-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 <A HREF="http://mmtsb.scripps.edu/cgi-bin/parallelopt">here.</A><BR>
-Ensemble properties can also be set from external data with
-<docmark>setprop.pl</docmark>. Ensemble properties may be queried with
-<docmark>ensprop.pl</docmark>.
 == Options ==