[chimerax-users] Feature request: combine while keeping chain IDs

[Eric Pettersen]

Hi Matthias,
	Thanks!  ISOLDE does indeed do a fantastic job of enhancing ChimeraX’s baseline modeling capabilities.
	Before discussing your suggestion per se, I wanted to mention a couple of approaches available right now to workaround the issue you mention.  The important thing to know is that forming the polymeric bond between two chain segments will combine them into one, with the resulting chain retaining the chain ID of the starting segment (for a peptide, the N terminal segment).  The approaches are:

1) If the chain segments are ready to be bonded (no missing intervening residues and it’s okay to move one relative to the other):  Instead of using combine, use the “build join peptide” command or the Join Models tab of the Build Structure tool to bond the termini.

2) If the chain segments are not ready to be bonded: use the combine command like before, but then for consecutive segments form a fake bond from the C terminal C of one to the N terminal N of the other with the command “bond appropriate-atom-spec reasonable false” or with the Adjust Bonds tab of the Build Structure tool.  This will combine them into a single chain.  After forming these bonds you can then break the bonds with ~bond or that same tab and the segments will still be one chain (you will see “missing structure” pseudobonds where the fake bonds used to be).

	So I could probably add an option to combine to retain chain IDs, which would basically do approach #2 above as a post-processing step to combine the segments with the desired ID.  The segments would need to have distinct residues numbers and the assumption would be to combine the segments in ascending residue number order.  If those assumptions aren’t true then you would have to resort to one of the “by hand” methods I just outlined.  I’ll open an enhancement-request ticket with you cc’ed so you’ll know when it happens.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Sep 14, 2022, at 9:25 AM, mailman-bounces--- via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> From: Vorländer,Matthias Kopano <matthias.vorlaender at imp.ac.at <mailto:matthias.vorlaender at imp.ac.at>>
> Subject: Feature request: combine while keeping chain IDs
> Date: September 14, 2022 at 9:10:48 AM PDT
> To: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>>
> 
> 
> Dear ChimeraX team, 
>  
> With the addition of Isolde, ChimeraX is now such a powerful modelling tool that I would like to suggest a new option for the “combine” command. It would be great if it were possible to specify that chain IDs are kept rather than being renumbered if both input models have the same chain ID (ideally this would only work if there were no overlapping residue numbers). This is very helpful if separately refined domains of proteins are put together in one PDB.
>  
> Thanks a lot in advance,
> Matthias
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