[Chimera-users] rmsd and display queries

[Elaine Meng]

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.