Subject: RMS Fits and Symmetries

From: [email-masked] (James A Given)
Date: Fri, 5 May 1995 14:50:54 -0400

RMS Fits For Structures That Have Symmetries

Dear CCL Participants:

  I have what I hope is a common problem. We are generating ligand
conformations for use in drug design. The ligands we use can
contain groups with various symmetries, e.g., benzene rings.  
Does anyone know how to take such symmetries into account when 
calculating RMS fit? 

  As a simple example of the problem that arises, imagine a 
molecule with a plane of symmetry through its center. If the 
molecule is flipped over and then superposed with the original, 
the RMS calculation of the difference between the two should be zero. But a naive
calculation of the RMS will not give zero, because the
pairing of atoms induced by the superposition is not the
identity pairing, i.e., the atom marked '1' in the original
will not be coincident with the atom marked '1' in the copy. 

  Perhaps the simplest case of this problem occurs when comparing
different conformations of a ring molecule. 

  Is there provision in standard software packages for handling this
problem? 

  Is there a stand-alone program that will accept as input a list of
symmetries (where each symmetry is given as a list of atom pairs to
be switched) and calculate the lowest value of the RMS that can be
obtained by first applying these symmetries? 

                            Jim Given
                            Center for Advanced Research in Biotechnology
                            Rockville, MD 

                            [email-masked]