Hi Tom,
Thanks, the "surface zone" does hide the map around the specified atoms. However, my question was how to apply that to a vseries? I want to use the "surface zone" to hide/delete part of the map to visualize internal details. Once I use the "surface zone" it should apply to all the frames of my vseries (20frames) and I should be able to play the vseries with part of the map missing. Hope it is clear.
Best
Rayees
________________________________
From: Tom Goddard
Sent: Friday, November 3, 2023 6:54 PM
To: Rayees Mattoo
Cc: Oliver Clarke via ChimeraX-users
Subject: Re: [chimerax-users] commandline to hide a map region or set a transparency in chimeraX
Hi Rayees,
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 zone #1 near #2/A distance 10 update false
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 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
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