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.edumailto: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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users