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 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.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Rayees,

Have you tried it with a volume series? A volume series is just a bunch of maps and you can apply the commands to all those maps. Say your 20 maps were #1.1,1.2,...,1.20 then

surface zone #1 near #2/A distance 10 update false

should work on all of them. They will have to have their surface shown so you will need to play through the series one time to create all the surfaces. If you are playing them with the vseries command you may need to use the cacheFrames option so that it doesn't get rid of the surfaces after it hides a volume. If something does not work tell me exactly what the error is.

One other tip is you can use the ChimeraX perframe command to run a command or series of commands each graphics frame before it gets rendered. So perframe can be used to run the surface hiding commands if for some reason doing the hiding to all of the series has a problem.

Tom

On Nov 5, 2023, at 11:25 PM, Rayees Mattoo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

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 goddard@sonic.net Sent: Friday, November 3, 2023 6:54 PM To: Rayees Mattoo rmattoo@stanford.edu Cc: Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu 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 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.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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