[Chimera-users] Calculation of RMSD between 2 PDB structures automatically

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 21 10:25:16 PDT 2009

Hi Sumitro,
This page in the User's Guide discusses the different superposition  
methods and tries to explain why you would use one or the other:

I explained a little bit about MatchMaker vs. match in my previous  
message, but that page has more information.

Only Matchmaker (available as both graphical interface and command)  
can automatically figure out which residues to pair with each other.   
We have found it to be effective even with fairly low % identities,  
but that is on entire proteins or domains. I would not expect it to  
be able to align shorter peptides correctly without high % identity.

As discussed in the previous message, I'm guessing you will need to  
use the "match" command, but you have to tell it which residues to  
match... it will not figure it out for you.

The "rmsd" command does not superimpose structures, it just reports  
the RMSD in their current positions (i.e. if they are far apart, the  
RMSD will be high even if they are copies of the same structure).   
Ensemblematch is only a graphical tool and not a command, and it  
works on ensembles where each structure contains the same atoms, just  
in different conformations.  I don't think either of those apply to  
your situation.

See the reply from earlier today for information on scripting:

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 Oct 21, 2009, at 4:46 AM, Sumitro Harjanto wrote:
> Hi,
> I have about 150 peptide structures in PDB format. I would like to  
> compare each of them with a Template Structure (also in PDB format)  
> and obtain an RMSD measurement for each comparison.
>  These peptides are similar in structures to the template but may  
> have very low sequence similarity/conservation.
>  So my question is:
> what is the command I should use given this scenario..? I was quite  
> confused with the many different commands such as: rmsd, match,  
> ensemblematch, matchmaker,… can anyone enlighten me on the  
> differences among them. I would like to find one which can align/ 
> superimpose 2 peptides and calculate RMSD (Ca or backbone)
> Is there a way to automate the process through scripting..?
> I’m still young with CHIMERA so please pardon my ignorance. =]
>  Cheers,
> Sum

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