Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287?
Hi Tristan, To specify a residue by all-numeric residue name, you can use the "name" attribute, e.g. in this label command: label ::name="287" height 2 Attribute specification: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> I didn't include "name" in the User Guide list of residue attributes, thinking people wouldn't need to use it in the command line, but then again maybe I should list it for situations like this... <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 16, 2021, at 7:12 AM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287? _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Cool! Admittedly an extremely rare situation - but the sort of thing that could be really frustrating when it does come up. Great to know there's a solution! ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 16 August 2021 17:45 To: Tristan Croll <tic20@cam.ac.uk> Cc: ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] All-numeric residue names Hi Tristan, To specify a residue by all-numeric residue name, you can use the "name" attribute, e.g. in this label command: label ::name="287" height 2 Attribute specification: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> I didn't include "name" in the User Guide list of residue attributes, thinking people wouldn't need to use it in the command line, but then again maybe I should list it for situations like this... <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 16, 2021, at 7:12 AM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287? _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Also, clicking "287" in the non-standard residue table for 2rg6, or using Select→Residues→287 resorts to using this exotic syntax in order to issue the appropriate "select" command. --Eric
On Aug 16, 2021, at 9:56 AM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Cool!
Admittedly an extremely rare situation - but the sort of thing that could be really frustrating when it does come up. Great to know there's a solution! From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: 16 August 2021 17:45 To: Tristan Croll <tic20@cam.ac.uk <mailto:tic20@cam.ac.uk>> Cc: ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] All-numeric residue names
Hi Tristan, To specify a residue by all-numeric residue name, you can use the "name" attribute, e.g. in this label command:
label ::name="287" height 2
Attribute specification: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>>
I didn't include "name" in the User Guide list of residue attributes, thinking people wouldn't need to use it in the command line, but then again maybe I should list it for situations like this... <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 16, 2021, at 7:12 AM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287? _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (3)
-
Elaine Meng -
Eric Pettersen -
Tristan Croll