CalcCluster

CalcCluster - reduce number of structures

CalcCluster expr expr expr

Takes a bundle of superimposed structures and determines a smaller number of structures that represent the same bundle as well as possible. This is done by clustering similar structures into groups, and taking the "central" structure of each group.

The command acts on all selected molecules and only considers the selected atoms of these molecules for the calculation.

The first argument gives the desired number of structures. The second argument gives the minimal RMSD between two resulting groups, where the RMSD between two groups is defined as the maximal RMSD between a member of one group and a member of the other group. The third argument gives the maximal RMSD of two members of a group. Due to these restrictions, the number of calculated clusters can be different from the one given as first argument.

The property "cluster" is set on all molecules that represent a group. From each group, the one with the smallest sum of RMSDs to all other members is chosen. A property (cluster1, cluster2, etc.) is also set for each member of every cluster.

This command supports groups.

EXAMPLE

CalcCluster 5 0.02 1

SelectMol, SelectAtom, Group, Fit, MeanMol

DATE

980817