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enscluster.pl
Usage
usage: enscluster.pl [options] tag
options: [-jclust] [-kclust]
[-maxnum value] [-minsize value] [-maxlevel value]
[-radius value] [-[no]iterate] [-maxerr value]
[-mode rmsd|contact|phi|psi|phipsi|mix]
[-contmaxdist value] [-mixfactor value]
[-l min:max[=min:max ...]] [-fit min:max[=min:max] | -fitxl]
[-selmode ca|cb|cab|heavy|all]
[-[no]lsqfit]
[-dir workdir]
[-opt file[:file]]
Description
This script applies a clustering algorithm to ensemble
structures. The options and functionality is very similar to
<docmark>cluster.pl</docmark>. The differences are that instead
of a list of files an ensemble tag is expected and the output is
stored in a file tag.cluster in the ensemble
data directory. The clustering options are also stored in and read
from the options file associated with the ensemble tag.
In addition to the parameters from <docmark>cluster.pl</docmark>
the parameter -dir is used to specify the ensemble directory.
With -opt other options files (other than the default one) can
be read in.
For fragment/loop modeling the residue range may be specified as
in <docmark>cluster.pl</docmark>, but if a residue range has been
stored in the ensemble configuration file previously clustering
will also only be based on the corresponding residue subset even
if -l is not explicitly given. Fitting for RMSD based clustering
is always done for the protein template surrounding the selected
residues.
The centroid output options are not supported in the ensemble clustering
script.
Options
- -help
- usage information
Examples
enscluster.pl -maxnum 3 -minsize 10 -dir data sample
performs hierarchical clustering for ensemble structure associated
with the sample tag.
The maximum number of clusters at each level is set to 3, subclusters
are recursively clustered again if they have 10 or more elements.