The same considerations apply to updating the electrostatic coloring each frame. To summarize the previous discussion when the trajectory goes to the next time step the surface is automatically recomputed and your coloring and transparency commands have to be done after that automatic surface recalculation. It is a bit tricky to make them happen after the surface recalculation and you should refer to the previous mailing list discussion to see examples of how that is done.

On Jan 30, 2024, at 3:54 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

update:

it seems that I could fix it via adding the transparency option
directly to color:

color byattribute kdh sel target s palette sandybrown:coral:orangered
novalue gray transparency 55

Just one extra question: how could I keep the coulombic electrostatic
surface (calculated using the command coulombic) in the same manner
for all frames ?

Il giorno mar 30 gen 2024 alle ore 12:28 Enrico Martinez
<jmsstarlight@gmail.com> ha scritto:

Dear ChimeraX users!

I am working on visualization of protein-ligand complex from MD
trajectory loaded as multiframe pdb via open coordset true

Here is my script:

#coloring ligand options
color ligand & C gold
style ligand sphere

#transparency
surface protein
color byattribute kdh protein target rs palette
sandybrown:coral:orangered novalue gray
transparency protein 5 surfaces
select zone ligand 4 protein
transparency sel 55 surface

The problem is only in the transparency which could be set only on the
first frame but then disappears when I browse movie. How could I
modify my scipr to keep the transparency on all frames ?

Many thanks in advance !

Enrico
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