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

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