[Chimera-users] Per-atom RMSD

Ibrahim Moustafa I.moustafa at psu.edu
Fri Oct 8 14:54:41 PDT 2010

Thanks Elaine, it works.


On 10/8/10 5:05 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Hi Ibrahim,
> Maybe I am not understanding your question correctly, but if you have two
> structures, the RMSD at each position is simply the CA-CA distance.  If you
> have three or more, it is more truly an RMSD.  But either way, yes, you can
> get that information after showing the sequence alignment of the superimposed
> structures.    
> First superimpose the structures using whatever method you prefer, even some
> other program.  Here is a discussion of methods in Chimera:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> Then use the Match->Align tool to generate a corresponding sequence alignment
> of 2 or more structures.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalig
> n.html>
> Then in the sequence alignment window, the "header" named RMSD can be
> displayed, if it is not already, by choosing Headers... RMSD from that
> window's menu.  The values are shown in a histogram over the sequences, but
> you can save them to a file as well, by choosing Headers... Save.
> More about sequence alignment headers including RMSD:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mult
> alignviewer.html#headers>
> These things are done interactively; currently there are no Chimera commands
> to do them. 
> 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 Oct 8, 2010, at 1:52 PM, Ibrahim Moustafa wrote:
>> Dear Chimera,
>>  I have a question regarding RMSD: I have two structures to superimpose
>> using certain residues; and I am interested to get the RMSD value for each
>> CA-atom in the structure. I wonder if there is a way to do that in Chimera?
>>  I think there is no direct way; but I wonder if there is a script that can
>> be used for that.
>> For the developer: It might be useful to have a tool that can directly do
>> that in Chimera
>>      Many thanks for help,
>>      Ibrahim

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