Hi Daniel & Tristan, Sequential coloring of a range of residues works in recent daily builds. The changes to allow doing this with either "color sequential" (aka "rainbow") or "color byattribute" with r:number were made about a week ago. E.g. in today's daily build: open 2gbp color byattribute r:number #1/A:20-50 palette rainbow - OR - rainbow #1/A:20-50 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 17, 2020, at 12:48 AM, Tristan Croll <tic20@cam.ac.uk> wrote:
It appears that Residue.number isn't registered in ChimeraX's attribute manager. That looks like a bug (will leave that to the ChimeraX team). You can work around it for now with a little tweak in the console (Tools/General/Shell):
from chimerax.atomic import Residue session.attr_registration._class_builtin_types[Residue]['number']=(int,)
Then your command should work - but I did run into a second bug using it when the ribbon is displayed:
color_by_attr rib_colors[:, 3] = residues.ribbon_colors[:, 3] if opacity is None else opacity ValueError: could not broadcast input array from shape (852) into shape (6733)
(but atoms are properly coloured) This can be worked around by repeating the command with a selection encompassing one atom per residue, e.g.
color byattr r:number sel&@CA target r
I'll report the issues via the bug tracker.
Tristan From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Daniel Larsson <daniel.larsson@icm.uu.se> Sent: 17 November 2020 08:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] sequential coloring of a range of residues
I can add that I only have problem with atom specifications with sequential coloring. Using the command "color #18/P:1-10 blue" works as expected and colors the designated range blue.
Regards, Daniel
On 2020-11-17, at 09:03, Daniel Larsson <daniel.larsson@icm.uu.se> wrote:
Hi,
I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options:
color sequential #18/P:1-10
This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P).
color sequential #18:1-10/P
This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10.
I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number:
color byattribute r:number #18/P:1-10
This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue
Am I doing something wrong? Is this feature not implemented yet? Is there a work-around?
Regards, Daniel
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