[Chimera-users] Question about "Color Zone" and "Render by Attribute"

Helge Paternoga helge.paternoga at googlemail.com
Sat Feb 1 06:04:38 PST 2014


Hello,

I have a question regarding the colouring of surfaces and their caps.

I am trying to recreate the colouring by hydrophobicity on capped 
surfaces as shown in (on the right side):

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey

So first I've opened the "Render by Attribute" dialog and assigned 
"kdHydrophobicity". This only coloured the surface and not the surface 
cap though.

I am assuming this is done by "Color Zone"? Indeed this colours the 
surface cap but I have one problem:

The colouring of the surface is different between "Render by Attribute" 
and "Color Zone" and I don't know why.
The differences are small but I would like to know which one is more 
accurate (intuitively I would say the one from "Render by Attribute"). 
I've played around with the radius of "Color Zone" but this doesn't 
achieve the same colouring as "Render by Attribute".

So my question is: How can I achieve the same surface colouring by 
"Color Zone" as in "Render by Attribute"?
Does it have something to to with "bondzone" or the hierachy in which 
the atoms apply their respective colour in "Color Zone"?

Thanks for reading!

Helge






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