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 Get Outlook for Android<https://aka.ms/ghei36> ________________________________ 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
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Elaine Meng -
Karim Rafie