[chimerax-users] Rotating/moving a chain to a different site

[Lohry, David]

Thanks!

That's what I needed. For some reason,  I had thought those commands worked differently on the model rather than chains but I tested what you wrote and it's what I need.


________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, February 27, 2023 9:54 PM
To: Lohry, David <dlohry at vols.utk.edu>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Rotating/moving a chain to a different site

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Hello David!
This answer is for ChimeraX:

To move something some exact number of angstroms or degrees, you would use commands.  The "move" (translate) and "turn" (rotate) commands each have an "atoms" option to specify moving only certain atoms, in this case one of the chains in your structure.  In the commands, you can also specify the direction of movement, axis of rotation, center of rotation, etc.

See help pages with the ChimeraX command "help" (e.g. "help move" or "help turn") or see the copies at our website here:
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmove.html&data=05%7C01%7Cdlohry%40vols.utk.edu%7C570cfbb717e64557519b08db19372a47%7C515813d9717d45dd9eca9aa19c09d6f9%7C0%7C0%7C638131496962065546%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=DZYHt0iLC3IS0rEPDcMh%2FaMRupDCuqSpYyGcOv2qRSY%3D&reserved=0>
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fturn.html&data=05%7C01%7Cdlohry%40vols.utk.edu%7C570cfbb717e64557519b08db19372a47%7C515813d9717d45dd9eca9aa19c09d6f9%7C0%7C0%7C638131496962065546%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LYvkaFU%2Fs%2BdRQPCyGWL4qDMuItmbAZUTnpOle0ezxL4%3D&reserved=0>

Example:
open 1zik
show atoms
name protb /B & protein
move y -20 atoms protb
turn z 35 center /B:14 at ca atoms protb

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

> On Feb 27, 2023, at 6:16 PM, Lohry, David via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello!
>
> I am working with a protein dimer with DNA from a crystal structure. The dimer is composed of 2 chains (chain A and chain B)
>
> I would like to be able to place one of the chains on a different region of DNA and at a slightly different position. The only tool that I could find was the Movement Mouse Mode in Chimera original.
>
> Is there a way to do this a bit more mathematically (keeping the chain in tact)? Move 50 angstroms in the x direction, rotate chain by 30 degrees, etc .
>
> Also, I need it to update the actual coordinates in the PDB when saved so it can't be something that just affects the visual output.
>
> Thank you!

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