Hi Oli and Kako,

Both your suggestions fixed it, thank you! What you suggest Kako is functionally equivalent, but can be done in a single step with adequate options to 'volume onesmask' (and with 'ones' plural in this command's name, as Oli points out!).

I indeed had this typo all along, which means enough ChimeraX for me for today...

Cheers,

Guillaume

Hey Guillaume!

I think its because the sphere isn’t a density volume until you do the following, then resample on grid.

volume onesmask #2 fullMap true valueType float32

volume resample [newspheredesity] ongrid #1

But I might be answering the wrong question 😊

Kako

From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Date: Thursday, 18 September 2025 at 15:10
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Generate a volume from a shape

Hello,

I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with:

shape sphere radius 30 center cofr

I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this:

volume onemask #2 ongrid #1

At which point I get this error: Expected a density maps specifier or a keyword

The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem.

Thank you in advance,

Guillaume

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