Hi Tom - tried this with the new daily and it works perfectly! This really helps, thanks!

I altered my "map_sphere" and "map_unsphere" shortcuts (https://github.com/olibclarke/chimerax-trimmings/blob/main/README.md) to use volume instead of surface, so one can quickly clip all maps around the cofr, set the contour using volume fastenclosevolume, then unclip.

Cheers
Oli

On Mar 9, 2024, at 11:49 AM, Oliver Clarke <olibclarke@gmail.com> wrote:

Hi Tom,

That should do the trick! I will adjust my shortcuts to use volume zone with the minimalbounds argument and then that should work nicely. Will test once the new daily is available. Thanks!

Cheers
Oli

On Mar 8, 2024, at 10:06 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Oliver,

One way you could do this is show just a subregion of all your class average volumes, then set all to have surface levels enclosing a specified volume, then show the full volumes, something like

volume zone #2-50 nearAtoms #1 minimalBounds true
volume #2-50 fastEncloseVolume 120000
volume unzone #2-50

The problem with this is that the encloseVolume option always works on the entire volume even if only a subregion is shown, and the fastEncloseVolume option is also supposed to work on the full volume but was in fact broken and gave the wrong answer if a subregion was shown.  But I just fixed this in the March 8, 2024 daily build so that encloseVolume and fastEncloseVolume apply just to the shown volume subregion.  Keep in mind that these options ignore the zoning, ie the hiding of the surface beyond a certain distance from the atoms, and only use the rectangular volume subregion being shown.  The subregion is set by the volume zone minimalBounds option.

The within_radius option modifying the encloseVolume options that you suggest is possible to implement, but it is so specialized that I don't think we are likely to find time to add that.

Tom


On Mar 8, 2024, at 3:20 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi ChimeraX-ers,

Finding an equivalent contour level for 3D classes in cryoEM can be challenging, particularly if the density histograms are sufficiently different that setting a single level does not suffice (and particularly when comparing many classes from a large classification).

The options "enclosevolume" and "fastenclosevolume" for the "volume" command are very useful for this (e.g. "volume #* fastenclosevolume 200000"), but fail in the presence of compositional heterogeneity (if there is more ordered stuff in one class and the volume is fixed, the contours will no longer be equivalent).

To address this, would it be possible to add a "within_radius" modifier for the "volume fastenclosevolume" command? This would mean one could then set a fixed volume to be enclosed by the contour within a set radius of either the center of rotation, or of an atom selection, making the contour levels at least locally equivalent (which is often what one wants for the purposes of comparison).

Cheers
Oli
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