CalcMatch

CalcMatch - calculate best matching structure parts

CalcMatch expr expr

Determines which parts of all selected molecules can be superimposed with the smallest RMSD, taking into account all selected atoms of all selected residues. The structures do not need to be identical, but the same number of residues with the same number of atoms each must be selected. The structures do not need to be superimposed before executing the command.

The first argument gives the minimal number of residues that must be superimposed, the second argument the maximal RMSD (to the mean) desired.

The algorithm is relatively simple, it superimposes the structures with the current set of atoms (starting with all selected ones), and in each step it leaves away the atoms from the residue that has the largest global displacement. This is repeated until one of the conditions given by the arguments is met.

A protocol of the progress, giving RMSD and largest displacement, is printed. All values are to the mean. At the end, an expression for selecting the superimposed residues for each molecule is printed. The property "match" is set on all these residues.

This command supports groups.

EXAMPLE

CalcMatch 50 0.7

SelectMol, SelectAtom, Group, Fit, CalcRmsd

DATE

960323