The old message you found was for Chimera. Here is how to save the map without the dust in ChimeraX. The simplest way is to set map values outside the displayed surface to zero.

A drawback of that is that the map drops sharply to zero outside the shown contour level which can make it look jagged. Another approach is to zero the dust, which can be done by showing only the dust surface and zero everything inside that surface. This uses the "surface invert" command that I just added and will be in tomorrow's ChimeraX daily build (not in 1.4).

This has the drawback that if you later show a lower threshold, new dust that has not been zeroed will appear.

Tom

On Jun 6, 2022, at 3:29 PM, Dai, Xin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX developers,

I'm trying to save a density map following the command "surface dust".
However, the map saved remains to be the original one. Is there any command to save the cleaned map?

I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html asking the same question using Chimera.
But unfortunately, it's not working for me.

Thank you,
Xin

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