[Chimera-users] How to use a colour-valued attribute?

Mungo Carstairs (Staff) g.m.carstairs at dundee.ac.uk
Thu Dec 4 00:25:47 PST 2014


Hi Elaine,

Thanks for that.

Having gone round the houses with setattr/defattr, I went back yesterday to retry the original 'color' command (incorporating tips for a better atomspec) and it is now as performant as the alternatives!  It seemed to 'degrade' a lot faster when I was using the original, naive atomspec with 'or' delimiters and a model specified for every position.

So I've gone round in a circle and ended up almost where I started, but wiser ;-).

Regards

Mungo

Division of Computational Biology
University of Dundee
http://www.jalview.org


________________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 03 December 2014 18:07
To: Mungo Carstairs (Staff)
Cc: chimera-users BB
Subject: Re: [Chimera-users] How to use a colour-valued attribute?

On Dec 3, 2014, at 1:30 AM, Mungo Carstairs (Staff) <g.m.carstairs at dundee.ac.uk> wrote:

> Thanks all.
> Tom, your suggestion of comma- instead or or-delimiter improves speed several times!
> Elaine, your point about specifying the chain is noted.
>
> Conrad, I didn't explain too clearly: my 'real' command is the 'non-contiguous' example (think Zappo colouring with some custom features colours on top).  The 'contiguous' example was just what I was using to explore behaviour of setattr / defattr / rangecolor.
> (Also by the way the REST API is working fine for me.)
>
> Instead of 'color' I am now using 'setattr' followed by 'rangecolor'.
> I tried both 'setattr' and 'defattr' (passing a temporary file) and didn't see any significant performance difference between them, at the scales I am testing so far (up to 3 models of 1600 residues).
>
> So I have what I need for now. But I'm still curious to know if / how you get Chimera to 'act on' (display) a colour-valued attribute.
>
> Best regards,
> Mungo

Hi Mungo,
Setting the color attribute with setattr or defattr does change the color immediately.  The problem in what you sent earlier:

setattr r color green #0:1-84.B

… is that there is no residue attribute named “color".  There are atom and molecule-model  attributes by that name (setattr a color …)  but the only per-residue color setting is ribbon color, name “ribbonColor” … thus you would want something like:

setattr r ribbonColor green #0:54.a,76.a

… and that would only color the ribbon, not the atoms/bonds.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops>

Actually I am mystified as to why this would be any faster than using the color command with the same atomspec (#0:54.a,76.a in the example above), but maybe the others who know more about the “guts” of Chimera can comment.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco




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