Dear Tristan,

 

Thanks a lot, that sounds great. I never considered using an ISOLDE simulation for that, that’s a cool idea. However, the coordinates wouldn’t end up being *exactly* the same as the reference model I assume?

 

Very much looking forward for the code you mention, for now I can continue with my own workarounds but I think this will be a great addition making Isolde and ChimeraX even better for model building.

 

Many thanks,

Matthias

 

From: Tristan Croll <tcroll@altoslabs.com>
Date: Wednesday, 11. October 2023 at 14:33
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>, Eric Pettersen <pett@cgl.ucsf.edu>
Cc: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model

I do have some code squirreled away in ISOLDE to do essentially this, but it needs a little "hardening" before I expose it to the user interface. If you have an urgent need let me know and I'll take you through how to access it via ChimeraX's Python shell.

 

Of course, if you're just talking about changes in coordinates and not actually changing the identities of any residues, then in ISOLDE you could just use the "source" model as a reference to set restraints on the target model and let a quick simulation do the rest.

 

-- Tristan

 

On Thu, Jan 12, 2023 at 5:49 PM Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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