Hi Dmitry, You don't say why you want to combine/split these chains, so there might be more direct way to accomplish whatever your ultimate goal is than my answers below, if we knew what your goal was. You combine chains by using the 'bond' command (or Build Structure tool) to form the C→N bond (or O3'→P bond for nucleic acids) between the chains. ChimeraX will combine them into a single chain. Splitting chains is uglier because ChimeraX knows that the residues in a chain form a chain even if you delete connecting bonds or even entire residues. The recipe would be to open multiple copies of your model. In the first copy, in the chain you want to split delete everything but the first "segment" you want split off. In the second copy delete everything but the second segment (and all other chains if there are any). So on and so forth. Then use the "combine" command to combine the models into one. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Jul 17, 2024, at 9:33 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues,

I have a lot of chains that I want to combine just in 1. How to do that?

And vice versa – I have 1 chain, and I want to split it into several.

Thank you in advance, Kind regards, Dmitry _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Dmitry, I thought you meant combining multiple chains into a single chain. However, if you instead meant combining chains that are in different models into a single model (still with multiple chains), see command "combine": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> Then if these chains have different chain IDs, it is easy to split that single model into multiple models again, one for each chain, with "split": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 20, 2024, at 3:50 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello Eric, Thank you for your answer. Following up combining and splitting chains topic I would like to specify more details. My question is connected to modelangelo output where one gets the separate chains. I would like to combine those chains in one structure. But maybe later I may need to divide the complete structure on chains again. Kind regards, DmitryFrom: Eric Pettersen <pett@cgl.ucsf.edu> Sent: 17 July 2024 19:26 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] combining and splitting chains

Hi Dmitry, You don't say why you want to combine/split these chains, so there might be more direct way to accomplish whatever your ultimate goal is than my answers below, if we knew what your goal was. You combine chains by using the 'bond' command (or Build Structure tool) to form the C→N bond (or O3'→P bond for nucleic acids) between the chains. ChimeraX will combine them into a single chain. Splitting chains is uglier because ChimeraX knows that the residues in a chain form a chain even if you delete connecting bonds or even entire residues. The recipe would be to open multiple copies of your model. In the first copy, in the chain you want to split delete everything but the first "segment" you want split off. In the second copy delete everything but the second segment (and all other chains if there are any). So on and so forth. Then use the "combine" command to combine the models into one.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Jul 17, 2024, at 9:33 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues, I have a lot of chains that I want to combine just in 1. How to do that? And vice versa – I have 1 chain, and I want to split it into several. Thank you in advance, Kind regards, Dmitry