"zone" near MULTIPLE residues in ChimeraX
Dear ChimeraX team,
I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve
Hi Steve, With “volume zone” you can specify any set of atoms.
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone
For example,
volume zone #3 near #2/A:54-56,75 range 5
The “volume zone” command is in the “see also” list on the page you were viewing; I try to cross-reference each page with a list of related features, but sometimes the list is long and/or easy to skip over. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 3, 2020, at 12:08 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team,
I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve
Forgot to answer all facets of the question, sorry. As you probably saw, "volume zone" is for the density map. For atoms and residue labels in a zone, you could just “show” and “label" using a zone specifier, e.g.
hide atoms; label delete show #2/A:54-56,75 :<5.0 label #2/A:54-56,75 :<5.0
See zone atom-specifier examples: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
The reason that there is a “zone" command that does all 3 types of zones for a single residue is to go with a mouse-mode that does it with a single click.
I hope this helps, Elaine
On Mar 3, 2020, at 12:14 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Steve, With “volume zone” you can specify any set of atoms.
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone
For example,
volume zone #3 near #2/A:54-56,75 range 5
The “volume zone” command is in the “see also” list on the page you were viewing; I try to cross-reference each page with a list of related features, but sometimes the list is long and/or easy to skip over. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 3, 2020, at 12:08 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team,
I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Steve,
It is a bit weird that this command only allows a zone around 1 residue. That is because it is simply the command version of the zone mouse mode where you click on a single atom and it shows the zone around the residue that atom belongs to. The mouse modes in ChimeraX issue equivalent commands, so this zone mouse mode needed a command version.
As Elaine mentioned you can show the density just near any set of atoms or residues with the "volume zone" or "surface zone" commands, and also you can label just the nearby atoms using zone atom specifiers to specify the residues within a certain distance of your 3 ligands of interest when using the label command.
Tom
On Mar 3, 2020, at 12:08 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team,
I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Steve Chou -
Tom Goddard