[Chimera-users] mmaker question

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 21 11:31:58 PDT 2014

Hi Joshua,
If you are fine with CA atoms only, approach (B) may be easier than using the "rmsd" command, especially if the structures have different numbering and/or contain different numbers of residues.  The problem with selecting and using "sel" in the command is that unless you picked atoms one by one, it isn't an ordered selection and you wouldn't necessarily get the desired pairing.  If you get some ridiculous RMSD, that is definitely the problem.  Instead you would need to use specification by residue numbers and atom names in the command line.  Whereas mmaker figures out pairing for you, the "rmsd" (and "match") commands do not, and you have to specify the atoms in corresponding orders. For CA-only calculations, approaches (B) and (C ) both done correctly will give the same result.

Command-line atom specification:


On Aug 21, 2014, at 11:22 AM, Joshua Broyde <jb3401 at c2b2.columbia.edu> wrote:

> Elaine, 
> Thanks for the help. I was looking for something like C, so I guess I will just select the C alpha atoms and get the RMSD.
> Sincerely,
> Joshua Broyde 
> ----- Original Message -----
> From: "Elaine Meng" <meng at cgl.ucsf.edu>
> To: "Joshua Broyde" <jb3401 at c2b2.columbia.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Sent: Thursday, August 21, 2014 2:00:44 PM
> Subject: Re: [Chimera-users] mmaker question
> Hi Joshua,
> Not sure I understand the question.  I'll try to answer some possible interpretations, but if I didn't answer your question, feel free to write back!  
> (A) To use your own sequence alignment to define the residue pairing for superposition and RMSD calculation, just open your alignment, make sure both structures are associated, and then from the Multalign Viewer menu (the menu of the window showing the sequence alignment) choose Structure…Match.  There are some additional options in the resulting GUI.   You could use the pairwise alignment from a previous mmaker command with "show true", if that helps. 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#superposition>
> (B) To just calculate the RMSD of structures in their current positions WITHOUT moving them, again starting with an alignment in Multalign Viewer with both structures associated, use the mouse to draw a region (which could be a single box in the alignment, or multiple disjoint boxes if you use Shift-drag) then from the Multalign Viewer menu choose Info…Region Browser.  The resulting dialog will show the RMSD for the region you defined with the mouse.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regionbrowser>
> (C ) The above use the Multalign Viewer graphical interface, not commands, and use only CA atoms.  There is also a "rmsd" command to calculate RMSD between 2 sets of atoms in their current positions without moving (it does NOT calculate the best-fit RMSD, just uses the current positions).  It would be harder to use because now you have to specify all the atoms in the command, e.g. if the residue numbering is different in the two structures, you would have to list the residue ranges.  You could specify any atoms common to both structures, not just CA atoms.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
> Best,
> 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 Aug 21, 2014, at 8:49 AM, Joshua Broyde <jb3401 at c2b2.columbia.edu> wrote:
>> Hi again,
>> I was wondering if the mmaker command had an option (or if there is some other way within chimera) of reporting the RMSD (as calculated by mmaker) of an alignment without actually superimposing one structure on the other. The reason that I am doing this that for a group of structures I can see with mmaker that they superimpose very well, but I want to show that when you compute the RMSD of those same structures when each is bound to a partner they are not quite as well aligned.
>> In essence, what I want mmaker to do is not really realign the structures for me, but to calculated the RMSD of an alignment that I provide it.
>> I looked at the mmaker command page but I couldn't seem to find an option for this.
>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html
>> Thanks again, and Chimera is a wonderful piece of software!
>> Sincerely,
>> Joshua Broyde
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>> Chimera-users at cgl.ucsf.edu
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