You cannot select just part of a map surface so you have to hide the patches in a tricky way. Here is how. The "surface zone" command lets you show the surface just near some specified atoms. You want to do the opposite hide the surface near atoms and there is no option for that (although I should add one). Instead you can show the surface just near the atoms then use the "surface invertShown" command to hide that part and show the rest. With map #1 and atomic model #2
surface invert #1
I use the "update false" option in the zone command otherwise a change to the contour level causes the original zone to be shown instead of hidden.
To make the surface transparent you could use the "color zone" command that colors a surface to match nearby atoms, it also set the surface transparency to the atom transparency. So for example you can make the surface transparent near chain A using
transparency #2/A 50 atoms
color zone #1 near #2 distance 10
But you probably don't want the atoms to be transparent. In fact ChimeraX cannot show two levels of transparency, so you won't see the transparent atoms under the transparent surface. You can change the atoms back to opaque
transp #2/A 0 atoms
or you could have two copies of your structure open and make one copy transparent and not displayed and just use that copy in the color zone command.
Tom
On Nov 2, 2023, at 3:25 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I was wondering if there is a command line in chimeraX to hide a region of the map. To be more specific if I have to hide map around a model #1 chain A, how could I do that? Also, using the same case how do I set a transparency of 50% for the map around the chainA model #1? Actually, I want to make a movie of the vseries where I need to hide/delete/transparent some portion of the map to show the internal details of the map while playing the vseries. Any suggestions are welcome.
Best
_______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/