[Chimera-users] how to calculate RMSD

[Elaine Meng]

> On Jun 30, 2021, at 7:19 AM, lufeiyu at jlu.edu.cn wrote:
> 
> Dear Sir/Madam:
> 
>    I have a question about the analysing of the docking. I docked a peptide to the receptor using GALAXYpepDOCK. The results uncontained the scores of RMSD. Some literatures reorted the UCSF could calculate the RMSD. But I didn't get the way after reading the tutorials. Please help me to figure out how to obtain the RMSD of a docking structure .Thanks vwry much. Best wishes for you.
> 
>                                           sincerely yours
>                                              Feiyu Lu


Dear Feiyu Lu,
The chimera-users at cgl.ucsf.edu address is recommended for asking questions about how to use Chimera.  I CC'd it here, so you do not need to send your question again.  (Or if you are using ChimeraX, you should use chimerax-users at cgl.ucsf.edu in the future for asking questions.)

An RMSD measures the difference between two different locations of a set of atoms.  So in Chimera you would need to open not only the docking results, but also the position of that peptide that you want to use as reference to calculate their RMSD.  Then, you can use the "rmsd" command to compare them.  I cannot give an exact command since I don't know the model numbers you will have, but an example if you had the comparison peptide open as model #3 and the docking result models are #1.1, #1.2, #1.3 ... then your commands could be:

rmsd #3 #1.1
rmsd #3 #1.2
[...]

See rmsd command help:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

The results would be shown in the Reply Log (open from Favorites menu).   Also if you don't know what model numbers you have, look in the Model Panel (also can be opened from the Favorites menu).

Model Panel help:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco