Hi Dmitry, You can do the combining into one model with "combine" and the splitting into multiple models with "split", see links in my previous message. The "split" command can use residue ranges (not just chain IDs) so you can split it however you want even if it is one chain. However, I don't know if it makes sense to make it all one chain, but I think Eric already explained that part in his reply. The "changechains" command can change the chain ID, and "rename" can change the model name and ID: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine

On Jul 25, 2024, at 9:05 AM, Dmitry Semchonok <semchonok@gmail.com> wrote:

Dear Elaine, Thank you for your answer. You were right. I meant to combine chains inside 1 model so that there would be only 1 model with 1 chain (instead of multiple). Can we rename all of them to 1? And vice versa — when there is one model, and one wants to split it into domains (chains)? Any ideas? Thank you. Kind regards, Dmitry

Ps. Sorry, I can not send the emails with illustrations to ChimeraX somehow.From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 22 July 2024 18:10 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] combining and splitting chains 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

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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

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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