You have hit on the right way to do this in ChimeraX. Color the connected surface pieces you want to use in your mask with the Blob mouse mode (menu Tools / Volume Data / Measure and Color Blobs), then use command "surface splitbycolor". In Chimera I guess you use sop split to make each connected surface piece selectable, then select all the ones you want in your mask, maybe hide those with sop hidePieces, then invert shown with sop invertShown, then maybe mask to that? ChimeraX doesn't do it in that way because surfaces in ChimeraX do not have a notion of separately selectable pieces like they had in Chimera. So coloring the connected pieces is the way to go.

On Sep 21, 2023, at 11:24 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks Elaine yep that works for masking, sorry I missed it on first look!

For “sop split”, I figured out that a combination of Measure & Color Blobs (https://www.cgl.ucsf.edu/chimerax/docs/user/tools/measureblobs.html), after setting a “pick blobs” mouse mode, with a subsequent “surface splitbycolor” more or less does the trick. Thanks!

Cheers
Oli

On Sep 21, 2023, at 1:58 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Oli,
For your second question, there is a "volume mask" command:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask>

Off to a meeting now, so haven't investigated the first part of the question yet...
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 21, 2023, at 10:50 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Is there a direct equivalent to the command “sop split” in ChimeraX? In the documentation for the “surface” command, I can see that there is an option to split by color, but not to split into individually selectable blobs.

We use this a lot in Chimera, as a quick way to make a starting point for a mask to use in refinement, so it would be great to have in ChimeraX too.

Also, is there an equivalent to the “mask” command from Chimera? I can’t seem to find it but perhaps it has a different name?

Cheers
Oli

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