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

Conrad Huang conrad at cgl.ucsf.edu
Tue Dec 2 10:17:36 PST 2014


You used two different ways to specify atoms for the "color" and 
"setattr" commands.  Have you tried comparing the speed for
	color #ffafaf #0:1-84.B
as opposed to
	color #ffafaf #0:1.B|#0:2.B|...
to see if there are performance differences?  The former specification 
requires testing each residue against a single sequence range, whereas 
the latter requires testing against many residue sequence numbers.  So I 
would expect the former to work faster than the latter.

Conrad

On 12/2/2014 2:10 AM, Mungo Carstairs wrote:
> Hi,
>
>
> 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
>
> etc
>
> 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?
>
>
> Thanks,
>
>
> Mungo Carstairs
>
>
> Division of Computational Biology
> University of Dundee
> http://www.jalview.org
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>



More information about the Chimera-users mailing list