[chimerax-users] Combining chain #1 and residue #2: naming issue

[Elaine Meng]

Hi Dmitry,
The "combine" command doesn't change any residue names or numbers, only chain IDs. 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> 

ChimeraX does not want to create models that have more than one of the same chain ID because there will be problems if they also have any overlapping residue numbers -- the residues would be no longer uniquely specifiable.   However, for modeling multiple domains separately into maps, we understand that there is now some need to allow combining models with the same chain IDs as long as there are not overlapping residue numbers.  The "combine" command does not yet allow this, but there is an open ticket:

#7608: Option to 'combine' to retain chain IDs
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7608>

If you want to combine models so that a chain keeps the same ID, instead of "combine" you would have to use "join  models" (part of Build Structure) to bond the N-term of one chain to the C-term of another.  However, that only does one chain at a time, and it will reorient/reposition one model relative to the other to form the bond.

With "renumber," if your chains already had numbering from seqstart 1, it will not change any numbers.  Maybe that is what happened in your case.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 26, 2022, at 1:17 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear colleagues,
> 
> I would like to add the residues to the secondary structure (residues come from similar structures and are aligned for the position). For that I use combine tool.
> 
> When I combine the secondary structure with the residues (combine #1 #2), in the new model the residues (#2) get arbitrary names and no longer belong to each of the main chains (#1).
> That creates a mass.
> 
> Could you please advise how to change the names of the residues so that each will belong to the corresponding main chain? (In the combined model I have chan A and residues G…ect )
> 
> I tried to use Renumber Residues tool but it did not work (renumber /A-F,I-M,X seqStart 1.  0 residues renumbered)
> 
> Thanks in advance.
> 
> Kind regards,
> Dmitry