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/