[Chimera-users] rmsd and display queries

goldmosh at fh.huji.ac.il goldmosh at fh.huji.ac.il
Sat Jun 9 13:02:03 PDT 2007

Elaine, hi.

Thank you very much for your detailed explanations about how to  
superimpose multiple structures. I need to do exactly the same, among  
several protein structures I am studying.
Thanks to Bala also, who asked the question before me.

-- Moshe Goldstein

Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Bala,
> (1) With EnsembleMatch you can superimpose multiple structures. Maybe
> what is confusing is that when you start EnsembleMatch it asks for
> one Reference PDB file and one Alternative PDB file.  Each of those
> PDB files, however, can contain multiple different conformations,
> separated by MODEL/ENDMDL records (for examples, see any NMR ensemble
> in the PDB, such as 1vm3).  In your case, to use EnsembleMatch you
> could put all of your conformations in one file separated by MODEL/
> ENMDL records, and then use that file as both the reference and the
> alternative.  Then you will have all pairwise comparisons for
> conformations in the file.  You can see how this works by opening
> 1vm3 (for example) and then specifying it as both the reference and
> the alternative. If you don't want to put your conformations together
> in one file, however, there are other ways to superimpose them and
> calculate RMSDs (more information below).
> (2) With EnsembleMatch you can specify the substructure or which
> atoms you want to use for the calculation in the "Parts to Match"
> area.  For example, if you wanted to use only alpha-carbons of chain
> A residues 8-95, you would enter this:
>   :8-95.A at CA
> EnsembleMatch manual page:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/
> ensemblematch/ensemblematch.html
> There is also an example at the end of this tutorial:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/
> ensembletut.html
> Here are some other ways to superimpose and calculate RMSD. All of
> the ways (including EnsembleMatch) are pairwise and give only
> pairwise RMSD values, but you can superimpose multiple structures by
> combining pairwise superpositions (match B->A, C->A to superimpose
> A,B,C).   There is currently no method to calculate a multiple (>2)
> structure RMSD.
> If you have the conformations as separate PDB files, you could use
> - the "match" command, and give the specific atoms (substructure) you
> want to match
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
> - the MatchMaker tool, which figures out for you which residues
> should be paired and then matches their alpha-carbons (assuming you
> have proteins)
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/
> matchmaker.html
> - the "matchmaker" command, which works the same way as the
> MatchMaker GUI
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html
> There are some examples of using "match" and "matchmaker" in the
> Images tutorial.
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/
> images.html#matching
> With MatchMaker/matchmaker, there is an option to show the sequence
> alignment in a separate window.  If you show that alignment, you can
> then highlight part of that alignment, choose Structure... Match from
> the alignment window, and choose "match active region only" to
> specify using only the CA atoms in the highlighted area(s).
> Yet another possibility: If you have too many conformations for
> EnsembleMatch (>~20) you could open them as a trajectory in MD Movie
> and then do an RMSD analysis.  This doesn't superimpose the
> conformations, however, just calculates all pairwise RMSDs using the
> atoms of your choice.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/
> framemovie.html
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/
> movie.html#rmsd
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Jun 6, 2007, at 5:25 AM, bala wrote:
>> 1) Basically i hav three conformations (only 3 pdb) of the same
>> molecule picked up from three different regions of a simulated
>> trajectory.
>> I hv to calculte rmsd and superimpose structure. I tried the
>> emsemble match but it seems that it can work on only two conformation.
>> Kindly suggest me how i can overcome this.
>> 2) Is it possible to create a substructure (subset) of a molecule
>> and do rmsd calcutn and superimposing only on the substructures for
>> the conformations i have.
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