Tool Set Documentation

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Revision as of 14:33, 12 August 2006


usage: [options] tag
options: [-jclust] [-kclust]
         [-maxnum value] [-minsize value] [-maxlevel value]
         [-radius value] [-[no]iterate]
         [-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]
         [-dir workdir]
         [-opt file[:file]]

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This script applies a clustering algorithm to ensemble structures. The options and functionality is very similar to <docmark></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></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></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.


usage information

Examples -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.