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

[Vorländer,Matthias Kopano]

Exactly! I am not aware of ISOLDE having this functionality, but wouyld be very greatful if it could be implemented in either ChimeraX or ISOLDE : )
Many thanks,
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 18:49
To: "Vorländer,Matthias Kopano" <matthias.vorlaender at imp.ac.at>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model

So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain?  This seems like something that the ISOLDE plugin would do already, but I'm not sure about that.

If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.

--Eric


On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

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<mailto:pett at cgl.ucsf.edu>>
Reply to: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Date: Thursday, 12. January 2023 at 18:17
To: "Vorländer,Matthias Kopano" <matthias.vorlaender at imp.ac.at<mailto:matthias.vorlaender at imp.ac.at>>
Cc: "chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu<mailto: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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