[chimerax-users] sequential coloring of a range of residues

[Tristan Croll]

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 at cgl.ucsf.edu> on behalf of Daniel Larsson <daniel.larsson at icm.uu.se>
Sent: 17 November 2020 08:20
To: chimerax-users at cgl.ucsf.edu <chimerax-users at 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 at icm.uu.se<mailto:daniel.larsson at 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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