[Chimera-users] Help with RMSD

Chee Wezen, Xavier xavier.chee11 at imperial.ac.uk
Fri Aug 9 11:51:05 PDT 2013

Thank you for your reply. I appreciate that. I've resorted to correct the Tripos file manually so then regenerate them using OpenBabel. I think that works as well.

Thanks !
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: 09 August 2013 19:17
To: Chee Wezen, Xavier
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Help with RMSD

Hi Xavier,
If you are just specifying the sets of atoms as #0 and #1, Chimera uses the atom names to figure out how the atoms pair.  However, even though your two files are chemically the same molecule, the atom names are all mixed up.  For example, in one molecule the carboxylate oxygens are named O2 and O3 while in the other molecule, they are named O and O1 (and the ones named O2 and O3 are in different parts of the molecule).  That's why the calculated RMSD is so high.  You would have to fix the names so that the corresponding atoms in the two structures would have the same names, or specify explicitly the pairing that should be used either by including all the names in the command in the corresponding orders (which would be a pain), or by selecting them in corresponding orders and specifying them in the command with the word "sel" "selected" or "picked" (which is also somewhat of a pain, but probably less than naming all the atoms in the command).

There are more details on how atoms are paired in the "rmsd" manual page:

If you receive errors saying you specified different numbers of atoms, you really did specify different numbers of atoms.  Sometimes this is surprising because the molecules are supposed to be the same, but there could be missing atoms, or alternate location atoms, or different amount of solvent.  You just have to be careful, and sometimes it takes a while to figure out why your specifications don't get the same numbers of atoms in the two structures.  You may need to specify residue numbers and/or atom names and/or delete solvent or alternate location atoms beforehand to get it to work.

More about command-line atom specification:

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 8, 2013, at 5:53 AM, Chee Wezen, Xavier wrote:

> Hello, may i know how to i use Chimera to calculate RMSD ? I opened the command line and typed "rmsd #0 #1" but the rmsd that i received from the two molecules above is way too high for something this superimposed. Can someone please suggest what should i do ?
> Meanwhile, i've also received error warnings for other molecules that i am testing (along the lines of "different number of atoms" found). this should not be the case as the molecules are identical to one another. Any help regarding this is much appreciated !
> Thanks !
> <Cocrys 442.pdb><SwissDock 442.pdb>

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