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

Mungo Carstairs g.m.carstairs at dundee.ac.uk
Tue Dec 2 02:10:27 PST 2014


This feels like a basic question but it has stumped me for a day now so here we go...

I'm exploring ways of programmatically setting colours to find the most efficient method.

This is for the 'custom coloured' case (residue-based colour schemes are not a problem).

The simple version is to send as many 'color' commands as there are colours in my (Jalview) sequence:

color #ffafaf #0:1.B|#0:5.B|#0:7-8.B|....;color #ffff00 #0:39.B|#0:44.B|#0:47.B|#0:77.B;

This works, but doesn't seem to scale up well for large/many structures - I start to see Chimera using 100% CPU for minutes at a time.

I'm trying instead to see whether setting a colour-value attribute is faster.

I can set the attributes ok with commands like

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


and confirm they are set with

list residues spec #0:1-84.B attribute color

but I can't figure out how to get Chimera to use the attribute value as the display colour.

'Render by Attribute' only seems to consider numeric (range-valued) attributes, not colour-valued.

I thought perhaps 'my' colour was just hidden in the colour hierarchy, but removing other colours doesn't seem to help.

What am I missing?


Mungo Carstairs

Division of Computational Biology
University of Dundee

The University of Dundee is a registered Scottish Charity, No: SC015096
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