[Chimera-users] combining two models into single model with two chains

[Elaine Meng]

Hi Ali,
I don't know what you mean by "sub-branches of that chain" -- if they are listed as two separate things in the Model Panel (e.g. #0.1 and #0.2), then it means they are two separate models.  You can show Model Panel from the Favorites menu.

If so, then you want to put them together into one model with two different chains. For that, see the "copy/combine" function in the Model Panel (in the menu under Favorites) or the "combine" command.  Details in the User Guide:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

If they are really only one model with one chain, then you can only change the ID of part of the chain if the two parts are really disconnected.  See Tools... Structure Editing... Change Chain IDs:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>

If they are NOT disconnected, you would have to manually edit the PDB file in some text editor first to add a TER between the parts.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. for general questions the better address is chimera-users at cgl.ucsf.edu CC'd here.  The chimera-dev address is for programming questions.

> On Nov 12, 2022, at 5:56 AM, Ali Doostmohammadi via Chimera-dev <chimera-dev at cgl.ucsf.edu> wrote:
> 
> Hi!
> I gave my protein to ClusPro for docking and it gave me the PDB file. For the next step, I need to upload to Prodigy, which requires me to separate the ligand chain and receptor chain to perform the analysis. But in the PDB file that I open in Chimera, there is only one chain, and ligand and receptor are divided as sub-branches of that chain, and Prodigy algorithm does not accept it.
> I wanted to know how to divide the protein and its receptor into two different chains?
> 
> Best regards!