Hi Pedro,

  Chimera had a nicer triangulation of the molecular surface than ChimeraX (but the Chimera molecular surface often crashed on large molecules), and that is why it gives nicer blurred conservation coloring than what Elaine showed.  The ChimeraX surface option gridSpacing (default 0.5 Angstroms) can make the surface triangles smaller which makes the the jagged edges less, but also makes the blur width less, so it almost looks like the sharp edges.  So I don't think that helps.

surface #1 gridSpacing 0.2
color zone #1 near #1 distance 5

  Tom

Here is the appearance of the color zone with grid spacing 0.5 versus 0.2.
grid_0.5.pnggrid_0.2.png

On Feb 14, 2024, at 9:11 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Pedro,
Coloring by conservation is a different situation than coloring by electrostatic potential.  The electrostatic potential is varying continuously in space (hence the gradual change in color), whereas the conservation is a single value per residue.  Thus, there is a single color for the surface patch that comes from the same residue.  So what you see is the true representation of the results.

In Chimera, it looked blended only as an artifact, because the surface triangulation did not try to make sharp boundaries per atomic patch; the jagged triangles from adjacent atoms were next to each other and made the color look blended.  

In ChimeraX, although you can turn off the sharp boundaries, doing that loses the linkage between the surface patch and the atom so you cannot directly color the surface by the property of the atoms (e.g. bfactor) or residues (e.g. conservation).

If you *really* want to try using the ChimeraX surfaces with sharp boundaries turned off, then you have to do a multistep process of coloring the atoms and then using color zone to color the surface to match the nearby atoms.  Even if you do that, you can see the jagged edges instead of smooth color blending because the conservation is a single value per residue (not continuously varying in space like electrostatic potential).

Here is an example with coloring by bfactor, but it would be analogous to do it for conservation.

open 2gbp
surface sharpBoundaries false
color byattr bfactor target a
color zone #1.2 near #1 dist 4

It is very ugly in my opinion, does not look like smooth blending.
<Screen Shot 2024-02-14 at 9.08.30 AM.png>

Maybe you could try to get a finer triangulation with other "surface" command options, but in my opinion it would probably be a waste of time.  You can see the difference with sharp boundaries true vs. false:

surface sharp true

<Screen Shot 2024-02-14 at 9.08.44 AM.png>

Again, the sharper boundaries are a more true representation of the values that you are trying to show.

I hope this makes sense,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 14, 2024, at 4:17 AM, Pedro Bule via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am trying to color the surface of my model according to sequence conservation. I opened the MSA, associated the proper sequence with the chain I wish to color, and then used the command "color byattr seq_conservation". But this results in the colors not blending at the surface, which is not very pleasant looking. Is there a way to make the transitions between adjacent colors smoother, similar to when we color the surface, for e.g., by electrostatic potential? In legacy chimera I used to follow the "Structure... Render by Conservation" in the Multalign Viewer and then choose the attribute mavConservation, which used to do the trick

Thanks in advance!

Pedro Bule

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