[Chimera-users] Question regarding RMSD

[Elaine Meng]

Hello Munira,
You didn't say how you superimposed the structures, but I'm guessing you used Matchmaker.  This is all explained in the help pages (command and tool) so it would be good to consult those before sending a question,  but I will try to summarize here:

By default there is iteration of the fit so that the parts that are more similar will be closely superimposed (allowing different parts like loops in different conformations to go their different ways).  In that case not all of the sequence-aligned positions will be used in the final fit.  So the two numbers are RMSDs calculated from only the positions used in the final fit, vs. for all the sequence-aligned positions regardless of whether they were included in the final fit.  You can turn on the matchmaker option to show the sequence alignment if you want to see it, and orange boxes on that alignment will show which positions were used in the final fit.

Press the "Help" button on the Matchmaker dialog to see the help, or view copies at our website here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

...or view command help with command "help matchmaker":
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

Iteration (pruning) is just an option.  You can adjust the option for tighter or looser pruning, or to turn it off entirely.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#matching>

Also, only CA atoms are used in  the RMSDs reported from Matchmaker.  If you want RMSDs calculated over all backbone, or all atoms (if they are really the same between the two structures) then one way is to use the "rmsd" command.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

Here is the help page overview of different superposition methods in Chimera:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

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

> On Aug 16, 2022, at 12:51 AM, ALI, MUNIRA (PGT) via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Good morning, 
> I have conducted a superposition between two of the same protein where one was obtained by X ray and the other was predicted by alphafold. I wanted to use the RMSD value of the alignment rather then just have qualitative results but I am unsure of how to interpret the values given by chimera.   
>   
> When I get the output of for example: RMSD between 189 pruned atom pairs is 1.164 angstroms; (across all 553 pairs: 10.750),  what exactly do these two outputs mean, which one should I be using and how exactly do I interpret this? 
> Kind regards, 
> Munira 
>