[Chimera-users] RMSD

Elaine Meng meng at cgl.ucsf.edu
Sat May 4 09:12:27 PDT 2013

Hi George,
After the crystal structure is superimposed onto the docking receptor (or maybe they are already the same protein), you can measure the RMSD between the ligand copies using the command "rmsd", see:


This is a general purpose command.  You can use it to measure RMSD without fitting between any two sets of atoms.  The only tricky part is that you may have to give not only the residue name but also the atom names in the command in the proper order if they are different between the two copies of the ligand, and you need to give the correct model number for the specific docking (e.g. #2.12 for 12th docking in results file opened as model 2).

I'm not sure where you were looking, but if you choose Help... Search Documentation from the Chimera menu and search for "rmsd", it is one of the top hits.  Maybe it wasn't clear that this was the correct command for the job.

Some docking programs will calculate this for you and output the RMSD values along with the other scores, but I don't remember the details.

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 May 4, 2013, at 6:40 AM, George Tzotzos wrote:

> Hi everybody,
> I am trying to measure the RMSD between a docked ligand and the corresponding ligand in an X-ray structure. I've been looking to find a way of doing this in Chimera to no avail. 
> I'd be grateful for any suggestions on how to do this. 
> Best regards
> George

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