Show map only around certain selection
Dear all,
I was wondering how to show part of a map only surrounding certain residues, i.e. I have coordinates for a multiple-chain PDB but I only want to show the electron density surrounding one chain.
Any help would be greatly appreciated.
Best,
Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden
Hi Karim, You can use the command "volume zone" with "newMap false": http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone
For example, if your map is #2 and your atomic model is #1 with chain of interest B, could be something like:
volume zone #2 near #1/B range 5 newMap false
(or "near sel" to use currently selected atoms instead of "near #1/B" to specify the chain directly). Then to go back to the full map display, command:
volume unzone #2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#unzone
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 2, 2020, at 9:36 AM, Karim Rafie karim.rafie@umu.se wrote:
Dear all, I was wondering how to show part of a map only surrounding certain residues, i.e. I have coordinates for a multiple-chain PDB but I only want to show the electron density surrounding one chain. Any help would be greatly appreciated. Best, Karim
Hi Elaine,
grand, thanks for the quick response.
Much appreciated.
Best, Karim
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________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, April 2, 2020 7:12:14 PM To: Karim Rafie karim.rafie@umu.se Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Show map only around certain selection
Hi Karim, You can use the command "volume zone" with "newMap false": http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone
For example, if your map is #2 and your atomic model is #1 with chain of interest B, could be something like:
volume zone #2 near #1/B range 5 newMap false
(or "near sel" to use currently selected atoms instead of "near #1/B" to specify the chain directly). Then to go back to the full map display, command:
volume unzone #2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#unzone
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 2, 2020, at 9:36 AM, Karim Rafie karim.rafie@umu.se wrote:
Dear all, I was wondering how to show part of a map only surrounding certain residues, i.e. I have coordinates for a multiple-chain PDB but I only want to show the electron density surrounding one chain. Any help would be greatly appreciated. Best, Karim
participants (2)
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Elaine Meng
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Karim Rafie