[Chimera-users] RMSD for two ligands

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 21 10:25:52 PDT 2013

Dear Pavithra,
Chimera cannot guess which atoms to use when there are different numbers of atoms in the two groups (#0 and #1). You would have to either

(A) include all the names of the atoms, in the order you want them matched, in the rmsd command. It would be something like: rmsd #0:15 at c1,c2,c3 #1:12 at c10,c5,c2  (if you wanted to match residue 15 atom C1 with residue 12 atom C10, residue 15 atom C2 with residue 12 atom C5, etc.). To see the atom names, show labels, for example command: label #0:15#1:12


(B) select all the atoms with the mouse (Shift-Ctrl-click) one by one, first the atoms you want to match in the first molecule, then the atoms you want to match in the second molecule in the corresponding order, and then use "sel" to specify the atoms in the rmsd command

The "rmsd" manual page can be viewed here (or by using command: help rmsd):

... and more about how to specify atoms in the command line:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 21, 2013, at 1:05 AM, Pavithra wrote:

> Dear Users,
> I want to calculate the RMSD of two ligand molecules of different atom counts but have a common scaffold.
> I tried rmsd #0 #1
> but I'm getting the error: unusual numbers of atoms chosen for evaluation.
> rmsd #0:15-17 #1:15-17
> atleast one atom must be selected.

> could somebody help me to find the RMSD between two ligands of different atom counts.
> -- 
> regards,
> Pavithra.K.B. 

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