Dear Eric,
Thanks for opening the ticket.
A related request regarding structural editing: I (and I suspect many others) often use ChimeraX to combine fragments of a chain from different models into a new model.
For example, if model #1 contains residues 1-100 and residues 400-500 of chain A, and model #2 contains residues 200-300 in chain A, that I would use combine #1 #2 to generate a complete PDB. This will change the chain ID of what used to be chain A in model
#2 to a new ID. Using changechains allows one to generate the compete chain A, however the resulting chain A is not correctly formatted in the PDB file. It will list residues 1-100, then reisdues 400-500, then residues 200-300, in that order. This destroys
pseudobond display and also messes with certain sequence operations. It would be great if in such a case the resulting PDB file would be correctly formatted, so that residues appear in the the PDB file in the order of they sequence number.
Many thanks,
Matthias
From:
Eric Pettersen <pett@cgl.ucsf.edu>
Date: Tuesday, 17. January 2023 at 22:40
To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Okay, I have opened an enhancement-request ticket in out bug-tracking database for this (https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323).
It may take awhile before it gets implemented -- it is competing against quite a few other development priorities.
--Eric
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 : )
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.
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
-
delete #1/A:1-10
-
select #2/A:1-10, save a pdb file with only the selected residues
-
Open this new PDB file (model #3)
-
combine #1,3
-
Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4
-
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?
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.
UCSF Computer Graphics Lab
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.
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