[Chimera-users] rmsd

[Elaine Meng]

Dear Altaira,
It is recommended to send questions to chimera-users at cgl.ucsf.edu (CC’d here) to ensure a reply.

As you can see from the log, one value is between 1733 pairs and another is between 421 atom pairs. 

The reasons matchmaker uses fewer atoms:
(1) it only uses one atom per residue, CA for amino acids
(2) in matchmaker, you used pruning which doesn’t use all sequence-aligned pairs, just the ones that end up closest in space

Also, matchmaker moves the structures, so unless you did the exact same matchmaker before the rmsd, the structures would be in different positions for the two RMSD calculations.  If the position is exactly the same, then to get the same RMSD from the two, you would have to specify in the rmsd command alpha-carbons only of all of the same residues that are sequence-paired in the matchmaker alignment (there is a matchmaker option to show that alignment) and use matchmaker without pruning (another option).  It would probably be difficult to list all the numbers of the matchmaker sequence-aligned residue pairs in the rmsd command.  You just have to understand which value you want and thus which method you want to use.

To understand the methods and their similarities/differences you would need to read their descriptions, see here and links therein.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

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


> On Apr 11, 2018, at 1:33 PM, Dearborn, Altaira (NIH/NIAMS) [E] <altaira.dearborn at nih.gov> wrote:
>  
> Dear Dr. Meng,
>   I calculated the rmsd using matchmaker and the rmsd command as you recommended in the thread below. I am getting vastly different values, 0.421 versus 25.274 angstroms and the number of atom pairs are different as well. Is there an option in the rmsd command that I am missing?
> Thank you,
> Altaira Dearborn
>  
> From the log:
> Executing rmsd ['sel']
> RMSD between 1733 atom pairs is 25.274 angstroms
>  
> Matchmaker combined-coot-2.pdb, chain A (#0) with 5dhv-Dimattia2016-23.pdb, chain A (#1), sequence alignment score = 607.3
> with these parameters:
>                 chain pairing: ss
>                 Needleman-Wunsch using BLOSUM-62
>                 ss fraction: 0.3
>                 gap open (HH/SS/other) 18/18/6, extend 1
>                 ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
>                 iteration cutoff: 2
>  
> Matchmaker combined-coot-2.pdb, chain B (#0) with 5dhv-Dimattia2016-23.pdb, chain B (#1), sequence alignment score = 563.1
> with these parameters:
>                 chain pairing: ss
>                 Needleman-Wunsch using BLOSUM-62
>                 ss fraction: 0.3
>                 gap open (HH/SS/other) 18/18/6, extend 1
>                 ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
>                 iteration cutoff: 2
> RMSD between 226 pruned atom pairs is 0.421 angstroms; (across all 226 pairs: 0.421)
>  
>  
> [Chimera-users] rmsd
> 
> Elaine Meng meng at cgl.ucsf.edu 
> Tue Nov 8 08:56:43 PST 2011
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> Dear Simone,
> Yes, there are many possible ways to calculate protein-protein RMSD in Chimera.
>  
> If you want Chimera to figure out the fit and superimpose the proteins for you, try MatchMaker: this uses the sequences and helix/strand locations to figure out how to superimpose the proteins, then reports RMSD and how many alpha-carbon pairs were used to calculate the RMSD.  MatchMaker is in the menu under "Tools... Structure Comparison."   It has several options.  The RMSD would be given in the Reply Log (in menu under "Favorites").
>  
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> 
>  
> If you want to tell Chimera specific residue numbers and atoms to fit, instead use the "match" command:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>  
> Or, if you do not want to superimpose, only calculate the RMSD in the current non-fitted positions, the "rmsd" command:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
>  
> Or, if you have a molecular dynamics trajectory or NMR ensemble of many copies of the same structure, there are additional methods for calculating all-by-all RMSD values.  
>  
> Discussion of all these methods and links to more details:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>  
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>  
> On Nov 8, 2011, at 2:08 AM, sdimicco wrote:
>  
> > Dear Chimera developers, 
> > is it possible to calculate the rmsd between two proteins by the softwere? How can I do it? 
> > Thank you in advance.
> > Simone
>  
>  
>  
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