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

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 3 09:43:24 PST 2014

Hello Helge,
I had mis-remembered that it was possible to color *only* the cap with Color Zone.  Experiments just now revealed that it does not let you choose the cap surface separately; you can only color the whole molecular surface + cap together.   Also, in agreement with what you reported, I can see there are differences in the outer surface coloring between what you get from Render by Attribute and Color Zone.  I find that the Render by Attribute result looks better to me, but unfortunately there is no choice if you wish to color the cap but to use Color Zone after using Render by Attribute to color the atoms.  It doesn't work to then re-color with Render by Attribute because that will un-color the cap.  I'll need to take a look at my tutorial and possibly revise the explanation; thanks for bringing this to my attention.

I don't think bondzone will improve this issue.  

I thought I had a solution, which was using the zone option of the scolor command instead of Color Zone, selecting only the cap part of the surface, and using "sel" to specify the surface in the command, but infuriatingly, that still recolored the outer surface as well!  Argh.

Sorry for the not-very-helpful answer; will let you know if further ideas arise.

On Feb 3, 2014, at 9:13 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Helge,
> Render by Attribute colors molecular surface points by some value of their associated atoms (or residues).  Color Zone colors surface (not necessarily molecular surface) points to match the closest atom center, so you would first have to color the atoms using Render by Attribute.  If you did indeed use Render by Attribute to color the atoms first, with exactly the same color mapping, I would expect only very small differences in the surface coloring result from Render by Attribute directly.   There still might be small differences because different atoms have different radii, and so the closest atom center to a molecular surface point might not be the atom explicitly associated with that point. 
> You should use Render by Attribute (or equivalently, command "rangecolor") to color any molecular surface, then Color Zone only for the cap and/or any nonmolecular surface such as a density isosurface.  The B-factor coloring image tutorial takes exactly that approach:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Feb 1, 2014, at 6:04 AM, Helge Paternoga <helge.paternoga at googlemail.com> wrote:
>> 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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