CYANA Command: molecules define

Parameters

parameters

Description

Defines a symmetric multimer with the monomers consisting of the residue range 1, residue range 2, etc. All monomers must have identical sequences. Alternatively the explicit residue range specifications can be replaced by a single asterisk “*”. In this case, the program will define the symmetric multimers automatically. If the command is used without any parameters, then a list of the defined multimers, and, with the option info=full, a list of the corresponding torsion angles and corresponding atoms in the different monomers is printed. Currently, only symmetric dimers are fully supported, and the subsymmetry parameter for the definition of the symmetry of the multimer (to distinguish, for instance, a “dimer of dimers” from a fully symmetric tetramer) must have the value 1. The molecules define command is most conveniently added to the init.cya startup macro together with other molecules commands that define identity restraints that minimize the difference between all corresponding torsion angles in the two monomers, and symmetry restraints that minimize the difference between selected corresponding distances that should be the same if the two monomers are oriented symmetrically relative to each other (see below). For example for a symmetric dimer consisting of monomer 1 with residues 1–53 and monomer 2 with residues 201–253, one may add the following lines to the init.cya file:

molecules define 1..53 201..253
molecules identity
weight_ide=0.03
molecules symdist "CA 1..53" "CA 201..253"
weight_sym=0.0025