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

[Ali Doostmohammadi]

Thank you so much! that was really helpful. my problem has been solved.

‫‪Elaine Meng‬‏ <‪meng at cgl.ucsf.edu‬‏> در تاریخ یکشنبه ۱۳ نوامبر ۲۰۲۲ ساعت
۲۰:۳۸ نوشت:‬

> 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!
>
>
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