Thank you very much Elaine !
Indeed it is a typical system for molecular dynamics with a lot of water on both sides from the bilayer.
With kind regards,
Enrico
Il giorno mer 26 lug 2023 alle ore 18:18 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hello, (1) Just like many other commands, you can specify the part you want to affect in the transparency command, for example:
transparency protein 95 target s transparency :OL,PA,PE 55 target s
That is what "spec" in the Usage line of the transparency help page means: https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html
There are many kinds of command-line specifier, like chain ID, residue numbers, atom names, categories like "protein", "sel" to mean the current selection, etc. as explained here: https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
(2) I don't know what the problem is with the water in your system. If there is a lot of water and it has hydrogens you could hide the hydrogens (unless you need to show them for some reason). If they are in the stick style then the water oxygens will just look like small balls.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 26, 2023, at 6:53 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX users!
I am dealing with the visualization of protein embedded into the plasmatic membrane (composed of water and lipids). Here is my script
preset publication 1 rainbow protein palette $palette
# for protein surface protein #color protein cornflower blue transparency 95 target s
# for lipids surface :OL,PA,PE color :OL coral target s color :PA coral target s color :PE orangered target s
hide bonds; hide atoms transparency 55 target s
- I would like to set different values of the transparency for the
surface of lipids and protein. For the moment I found only one possibility to set the transparency for the whole surface indicated above. Would it be possible to selectively apply a transparency command on the particular selection of the system ?
- how would it be better to visualize the water in the same system in
order to maintain the visibility of the protein ?
Many thanks in advance
Enrico