Using a cube with map eraser instead of a sphere is a good idea and a few others have asked about it. So far I have not had time to work on it, but here is the feature request ticket from 2 years ago. I added your email to that ticket so you will hear if any progress is made.

Is it important to be able to rotate the cube to any orientation? I would think so. That complicates things a bit since the sphere currently does not rotate so the mouse mode would need work, not sure how to allow rotation since the shift key modifier is already used to resize the sphere. Also the code will need to be able to mask out a cube region that is not aligned to the volume axes. Best to reply to the ChimeraX ticket email you should get, so your answer is recorded. None of it is too hard, but when we are buried in new feature possibilities of more widely useful things like AlphaFold 3 and have limited resources, these niche items like cube erasers don't get done. As usual code contributions from others are welcome.

On Jan 9, 2025, at 8:11 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

Hope the chimeraX team & community are having a great start to 2025!

There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask.

There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere?

Cheers
Oli
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