[Chimera-users] want to converge 20 pdb files of a trimer

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 7 16:08:10 PDT 2013

Hi Ashok,
As I said, you have to use the match command 19 times because it will only make a pairwise match.  You have to decide which one you want to use as the reference and then match each of the other 19 to the reference in a separate match command.

Also, your first command is wrong, should contain "-" instead of "," to use all the residues from 379 to 400 (instead of only two residues, 379 and 400). For example, if you want to make #0 the reference:

match #1:379-400 #0:379-400
match #2:379-400 #0:379-400
[ ... etc. 18 more times ...]

The above is if you had each NMR structure in its own separate PDB file. Usually NMR structures in the PDB are all in one file.  In that case, it would be something like:

match #0.2:379-400 #0.1:379-400
match #0.3:379-400 #0.1:379-400
[ ... etc. 18 more times ...]


> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic>

On Oct 7, 2013, at 3:57 PM, ashok rout wrote:

> Hi Elaine,
> Thanks for your reply. I am able to superimpose 2 pbd files by using command "match #0:379,400 #1:379,400", where #0 and #1 are 1st and 2nd pdb files. 379, 400 means I want to superimpose residues from 379 to 400.
>  After that I have problem (error: an even number of space-separated atom specs are required) when I am trying to superimpose 3 pdb files using command "match #0:379,400 #1:379,400 #2:379,400". 
> I am clearly writing you:
> I have 20 pdb files of the trimer. e.g 1.pdb, 2.pdb, 3.pdb .... 20.pdb
> Residues in the pdb file is from 369-410. I want to superimpose residues from 379-400.
> So what exactly the commands and steps.
> Thanks,
> Ashok
> On Mon, Oct 7, 2013 at 3:21 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ashok,
> Not sure exactly what you mean by "converge" ...
> (A) If you mean to superimpose (to put on top of each other), you would probably want to use either MatchMaker or the command "match."  The different methods for superimposing structures are described in this page and its links:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> With the "match" command you specify exactly which residues/atoms to use in the match. You would have to use it 19 times with the same single structure as reference (e.g. to superimpose 0.1 and 0.2, then 0.1 and 0.3, ...)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic>
> Matchmaker only uses CA atoms and doesn't require specifying which residues to use, but optionally you can restrict it to use only a certain section with the "Further restrict matching to current selection" option.  You can choose one structure as reference and the other 19 as structures to match.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
> (B) If you mean to calculate an average, you can do that with the MD Movie tool, after opening the NMR file as a trajectory:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> 1. download the NMR structure PDB file to some location on your computer that you will be able to find later
> 2. start MD Movie (in menu under Tools... MD/Ensemble Analysis)
> 3. choose to open "PDB, single file" and browse to open the NMR structure file
> 4. from the MD Movie menu, choose "Analysis... Average Structure"
> Be aware this is a simple Cartesian coordinate average and the result may be distorted. I don't think you can average just some part. Just average the whole thing and then you can delete the parts you don't want later.
> 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 7, 2013, at 2:38 PM, ashok rout wrote:
> > Hi,
> >  I have a nmr structure of a protein which is a trimer. I want to converge 20 pdb files of the trimer, by Chimera. And also want to converge a specific region of the 20 pdb files of the trimer.
> > Can you please assist me how to do this??
> > Thanks,
> > Ashok
> -- 
> thanks & regards,
> Ashok
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