[Chimera-users] PDB post-processing

Elaine Meng meng at cgl.ucsf.edu
Wed May 25 10:18:18 PDT 2016


Hi Gleb,
Take a look in the menu: Tools… Structure Editing  There are tools and commands to “Change Chain IDs” and “Renumber Residues,” see

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.html>

However, I don’t know if you can do everything you described, since the chain ID will change for a whole chain, not just part of a chain.  You would need to indicate that parts are really separate chains, perhaps by manually editing TER into the PDB file in those places, or deleting the covalent bonds between them, if any.  If these tools don’t do what you need, you may have to do the residue/chain editing manually or with a script outside of Chimera.  There are some web servers, e.g. <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>  but that approach is not really practical if you have a lot of files to process.

For superposition, you’d probably use matchmaker or match, see explanation here and links therein:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

There is a “combine” command to make >1 model into 1 model, but I don’t think that is what you need...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

Instead, when you have the multiple models superimposed, just save PDB (File menu or command “write”).  There is a PDB-saving option to save a single multimodel  file, similar to an NMR ensemble.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

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 May 24, 2016, at 12:58 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera users!
> 
> After some post-processing of MD simulation I have extracted from the
> trajectory several snapshots as individual pdbs which I need to
> 1-  to re-assign information regarding chain letters (which was lost
> after some operations on pdbs)  for all of those structures assuming
> that within each of these pdbs residues are ordered correctly e.g from
> (1-104 which
> should be chain A) than from 1-100 (it should be chain B), than 1-70
> (in should be chain C) etc.
> 
> 2- superimpose and combine all of the pdbs within one model in nmr-like format.
> 
> Thanks for help!




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