[chimerax-users] Surface Coloring

[Elaine Meng]

Hi Juliana,
The appearance in ChimeraX is actually a more accurate representation of coloring by Kyte-Doolittle hydrophobicity values.  In both Chimera and ChimeraX, there is a simple lookup table by amino acid type (e.g. leucine always gets the same number), and then the surface for each amino acid is colored to show that value.  Chimera shows a more blurry edge because some of the surface triangles cross between different residues, but it's really an artifact.  ChimeraX shows a sharp edge because the surface triangles are drawn so that they only belong to one atom instead of crossing between more than one atom.

Two thoughts:

(1) MLP is different and actually varies in space on a 3D grid, so you will get gradual changes in color.  So my first thought is why not use MLP?  If you don't like the coloring scheme you can use other colors, e.g. command

mlp palette dodgerblue:white:orangered range -20,20

(2) If you really want to just use a simple lookup table that always gives the same value for the same type of amino acid but try to make it look more like the result in Chimera, you would have to force the surface creation to make triangles that cross between atoms, then color the atoms by attribute, and then use yet another color command to make the surface colors match nearby atoms.  You can't color the surface in a single command because this type of surface (with triangles that go with more than one atom) isn't directly associated with the atoms/residues or their attributes.

Sounds like you already found the ChimeraX command file to assign Kyte-Doolittle hydrophobicities and color by attribute:
<https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc>

The last two commands in that file are:

surf protein; hide protein atoms
color byattribute kdh protein target rs palette dodgerblue:white:orangered novalue gray

To get jagged boundaries you would need replace those with something like the following, where #1 is the surface model (change that as needed if your surface is a different model number):

surf protein sharp false; hide protein atoms
color byattribute kdh protein target a palette dodgerblue:white:orangered novalue gray
color zone #1 near protein distance 3

It still doesn't look exactly like it does in Chimera, but again, how it looks in Chimera is really an artifact anyway.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 7, 2021, at 11:27 AM, Juliana Glavina via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear All,
> I am moving from Chimera to ChimeraX and I am trying to reproduce some of things that I used to do in Chimera.
> I managed to colour the surface by the kdHydrophobicity scale. However, the coloring is discrete with sharp edges between the residues. I was wondering if it was possible to smooth the edge between two different colors on the surface - similar to mlp but with customized attributes.
> Thank you very much in advance
> 
> UCSF ChimeraX version: 1.2.3 (2021-05-13)
> Ubuntu 20.04
> 
> Juliana