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

ashok rout ashok9869 at gmail.com
Mon Oct 7 15:57:13 PDT 2013

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.

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,
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