[chimerax-users] Feature request: replace residues in model with residues from other model

[Vorländer,Matthias Kopano]

Hi Eric,

Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would


  1.  delete #1/A:1-10
  2.  select #2/A:1-10, save a pdb file with only the selected residues
  3.  Open this new PDB file (model #3)
  4.  combine #1,3
  5.  Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4
  6.  The I would use the command changechains #4/B A and this would yield the result that I want

What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.

I hope that made it clearer?

Thanks a lot,
Matthias
From: Eric Pettersen <pett at cgl.ucsf.edu>
Reply to: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Date: Thursday, 12. January 2023 at 18:17
To: "Vorländer,Matthias Kopano" <matthias.vorlaender at imp.ac.at>
Cc: "chimerax-users at cgl.ucsf.edu" <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model

Hi Matthias,
I not familiar with "replace fragment", so I have a few questions.  Is it always the same number of residues in source and target?  Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)?  I assume you have to use the backbone conformation of the target.  Are the side chain angles preserved in any way?
It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab



On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Dear ChimeraX team,

Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.

Many thanks in advance,
Matthias
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