I will try to answer #1:

As I understand it, gridSpacing is really the only "quality" setting for surfaces. 

Decreasing the probeRadius doesn't change the quality of a solvent-excluded surface, it just changes the shape of surface to include smaller crevices.  The figure in the "surface" manual page shows how the probe radius affects the shape of the solvent-excluded surface:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

Surface calculation parameters are explained here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#parameters>

As explained in the link above, the "resolution" option does not apply to a solvent-excluded surface, but instead changes the calculation to a Gaussian surface.  Gaussian surfaces do not use the atomic VDW radii or probe radius, but instead the specified "resolution" and "level" values.

I hope this helps,
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 Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX users!
>
> I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
>
> 1- I've found that the quality of the surface could be mainly controlled using two options
> gridSpacing and probeRadius
> so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
>
> 2- Setting different degrees of transparency of different selections.
> In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
>
> # first color the entire membrane in blue
> color ~protein blue surface transparency 40
> # color only the headgroups in red  setting less transparency
> color :PC red surface transparency 80
>
> This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
>
> Thank you very much in advance
>
> Best regards
>
> Enrico
>
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