Hello Tom,
actually I have not found an explanation but sometimes transparency applied on the whole trajectory disappears without any explanation :-)
For example I apply it either via rainbow or color command on two monomers separately using the following commands:
# first show cartoons and color them using palette cartoon protein surface protein gridSpacing 0.5 rainbow :1-304 target c palette ^paired-12 rainbow :306-607 target c palette ^paired-12
# then add transparent surface for the same selection transparency #1 80 rainbow protein & :1-304 target s palette ^paired-12 transparency 90 rainbow protein & :306-607 target s palette ^paired-12 transparency 90
#color protein & :1-304 indianred target s transparency 90 #color protein & :306-607 royalblue target s transparency 90
Eventually If I change in the second selection string the number of selected residues (for second protomer) to protein & :305-607 (so selecting one more residue), it does not work at all and I see only surface without any transparency. Probably there is a bug somewhere (I am using UCSF ChimeraX version: 1.6.1 on local Ubuntu) ?
Cheers !
Il giorno mar 30 gen 2024 alle ore 19:45 Tom Goddard goddard@sonic.net ha scritto:
You asked the question about how to keep the transparency on a surface during trajectory playback in December and it was answered back then
https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...
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.
Tom
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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