[chimerax-users] RMSD command in ChimeraX

[Hrvoje Rimac]

Hi,

I was wondering if there is a command in ChimeraX which calculates RMSD
without first aligning the ligands (analog to Chimera command "rmsd"). The
problem is that the order of atoms in the two pdb files is not identical,
and in Chimera (1.14) the "rmsd" command (as well as the "match" command)
compares the first atom to the first atom, the second to the second etc,
regardless of their type (I checked this manually), so the calculated RMSD
is very high. In ChimeraX this mismatching problem is resolved, however
the only command I found was the "align" command which calculates RMSD
after aligning the molecules (as "match" match does in Chimera). Is there
a command that would calculate RMSD without aligning the molecules? This
wouldn't be a problem if I had 2 ligands to compare, but since I have more
than 900, it would be very time consuming to check and correct order of
all atoms.


P.S. I have attached the structures of the two ligands. The RMSD values
I'm getting are:
Chimera "match": 4.064
Chimera "rmsd": 4.147
ChimeraX "align": 0.252
The value I should get: 0.454



Best regards,
Hrvoje Rimac





Hrvoje Rimac, PhD.
Postdoctoral Fellow
Department of Medicinal Chemistry
Faculty of Pharmacy and Biochemistry
University of Zagreb
A.Kovačića 1, 10000 Zagreb
Croatia
http://www.pharma.unizg.hr/
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