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

[Daniel Larsson]

Many thanks!

Regards,
Daniel

> 17 nov. 2020 kl. 16:49 skrev Elaine Meng <meng at cgl.ucsf.edu>:
> 
> 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 at 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 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> 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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>>> 
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