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Difference between revisions of "enscluster.pl"
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This script applies a clustering algorithm to ensemble | This script applies a clustering algorithm to ensemble | ||
structures. The options and functionality is very similar to | structures. The options and functionality is very similar to | ||
| − | + | [[cluster.pl]]. The differences are that instead | |
of a list of files an ensemble tag is expected and the output is | of a list of files an ensemble tag is expected and the output is | ||
stored in a file <font color=#508060>tag.cluster</font> in the ensemble | stored in a file <font color=#508060>tag.cluster</font> in the ensemble | ||
data directory. The clustering options are also stored in and read | data directory. The clustering options are also stored in and read | ||
from the options file associated with the ensemble tag.<BR> | from the options file associated with the ensemble tag.<BR> | ||
| − | In addition to the parameters from | + | |
| + | In addition to the parameters from [[cluster.pl]] | ||
the parameter <B>-dir</B> is used to specify the ensemble directory. | the parameter <B>-dir</B> is used to specify the ensemble directory. | ||
With <B>-opt</B> other options files (other than the default one) can | With <B>-opt</B> other options files (other than the default one) can | ||
be read in.<BR> | be read in.<BR> | ||
| + | |||
For fragment/loop modeling the residue range may be specified as | For fragment/loop modeling the residue range may be specified as | ||
| − | in | + | in [[cluster.pl]], but if a residue range has been |
stored in the ensemble configuration file previously clustering | stored in the ensemble configuration file previously clustering | ||
will also only be based on the corresponding residue subset even | will also only be based on the corresponding residue subset even | ||
if <B>-l</B> is not explicitly given. Fitting for RMSD based clustering | if <B>-l</B> is not explicitly given. Fitting for RMSD based clustering | ||
is always done for the protein template surrounding the selected | is always done for the protein template surrounding the selected | ||
| − | residues. | + | residues.<BR> |
| − | <BR> | + | |
The centroid output options are not supported in the ensemble clustering | The centroid output options are not supported in the ensemble clustering | ||
script. | script. | ||
Revision as of 14:28, 30 July 2009
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
cluster.pl. 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 cluster.pl
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 cluster.pl, 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
- -jclust
- use j-cluster method
- -kclust
- use k-cluster method
- -maxnum value
- -minsize value
- -maxlevel value
- -radius value
- define cluster radius
- -[no]iterate
- iterate clustering method
- -mode rmsd|contact|phi|psi|phipsi|mix
- clustering mode
- -contmaxdist value
- -mixfactor value
- -l min:max[=min:max ..]
- cluster using specified residue range
- -selmode ca|cb|cab|heavy|all
- cluster using specified atom selection
- -[no]lsqfit
- -dir workdir
- use specified ensemble directory
- -opt file[:file]