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!
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://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html> Example: open 1zik show atoms name protb /B & protein move y -20 atoms protb turn z 35 center /B:14@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@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!
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@cgl.ucsf.edu> Sent: Monday, February 27, 2023 9:54 PM To: Lohry, David <dlohry@vols.utk.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Rotating/moving a chain to a different site [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] 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....> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....> Example: open 1zik show atoms name protb /B & protein move y -20 atoms protb turn z 35 center /B:14@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@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!
participants (2)
-
Elaine Meng -
Lohry, David