Hello, I'm playing around with the define axis command, and noticed that in the documentation the link to "plane-spec" does not lead to anything that defines how to specify a plane (help:user/commands/atomspec.html#othermodels). Or at least, I can't see it. The link to "point-spec" does take me to an informative page (help:user/commands/pointspec.html#point). Is the syntax for specifying a plane defined elsewhere? This is with 1.6.1. Cheers, Alexis
Hello Alexis, It works for me, although does not mention planes specifically, but lumps them as "nonatomic models": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#othermodels> "Nonatomic models such as nonmolecular surfaces or maps (volume models) can be specified in a more limited set of ways, namely: • hierarchical specifiers – model number • built-in classifications – sel (the current selection, which could include nonatomic models)" Examples: open 2gbp define plane ligand color #1.2 red (or if you want to select it by model number:) select #1.2 (or you can select in the graphics window with Ctrl-click, then refer to it as "sel") color sel cyan I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 2:52 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I'm playing around with the define axis command, and noticed that in the documentation the link to "plane-spec" does not lead to anything that defines how to specify a plane (help:user/commands/atomspec.html#othermodels). Or at least, I can't see it. The link to "point-spec" does take me to an informative page (help:user/commands/pointspec.html#point).
Is the syntax for specifying a plane defined elsewhere?
This is with 1.6.1.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thanks Elaine, I guess given the way the plane-spec was introduced in the "define" help page, following the "point-spec" as another alternative to "atom-spec" I wasn't expecting to land in the atom-spec page. I had even hoped that a plane could be defined using coordinates. But not to worry, I've got a sufficient workaround for what I need to do right now. I was just flagging it in case it was a documentation issue. Cheers, Alexis On Thu, Nov 16, 2023 at 3:48 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Alexis, It works for me, although does not mention planes specifically, but lumps them as "nonatomic models":
< https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#othermodels
"Nonatomic models such as nonmolecular surfaces or maps (volume models) can be specified in a more limited set of ways, namely: • hierarchical specifiers – model number • built-in classifications – sel (the current selection, which could include nonatomic models)"
Examples:
open 2gbp define plane ligand color #1.2 red
(or if you want to select it by model number:)
select #1.2
(or you can select in the graphics window with Ctrl-click, then refer to it as "sel")
color sel cyan
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 2:52 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I'm playing around with the define axis command, and noticed that in the documentation the link to "plane-spec" does not lead to anything that defines how to specify a plane (help:user/commands/atomspec.html#othermodels). Or at least, I can't see it. The link to "point-spec" does take me to an informative page (help:user/commands/pointspec.html#point).
Is the syntax for specifying a plane defined elsewhere?
This is with 1.6.1.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Alexis Rohou -
Elaine Meng