Thank you very much Elaine ! In fact, asI found that the probeRadius is useful for visualisation of the lipids in membrane systems since it could "shapes" their form better (as you have mentioned in your reply). BTW a I noticed decreasing the probeRadius also significantly requires more calculation time. Yours sincerely Enrico Il giorno ven 5 apr 2024 alle ore 00:48 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
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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