RFE: allow models to be immune to clipping

[Elaine Meng]

Mainly of interest for clipping a surface without clipping ribbons or atoms. I was trying to show the internal ligand-binding pocket of 3e8t without clipping the ligand atoms, which is difficult. Allowing clipping just the surface model (making the atomic model model immune) would better replace the useful functionality of Per-Model Clipping in Chimera1.

Could be implemented only for front/back (rotatable) planes, not hither/yon. Could be an option of clip, could be a model attribute, or could be a simple toggle to clip surfaces only vs. clip all model types. (There is also a ticket to rework the clip command, but I don't feel strongly about that.)

[Tom Goddard]

Doesn't it make more sense to just per-model clip the surface, instead of try to tell every other model not to clip? It sounds like your application is best addressed by per-model clipping. I planned on adding that some day, but is it a higher priority than the many other missing features?

[Elaine Meng]

yes, amongst the copious blather in the original message (sorry) I did say that one possible solution was  "could be a simple toggle to clip surfaces only vs. clip all model types”

I didn’t realize you had separate plans for per-model clipping … in my opinion the suggestion above would take care of 99% of the needed functionality of per-model clipping, even if it applied to all surfaces collectively.  I’ve only seen per-model clipping used for the purpose of clipping the surface and not the atomic model within the surface.

[Elaine Meng]

(...entering in the webform in hopes it will be more readable than the previous comment...)

As for priority, although I was highly frustrated by various blockers to making example images, I'll leave prioritization to you. Just wanted to get the request in the database. I didn't realize you had separate plans for per-model clipping and thought this enhancement (however implemented, whether as per-model susceptibility or surfaces-only toggle) would cover that functionality.

[goddard@…]

There are two parts to implementing per-model clipping.  First the code has to be able to clip some models and not others.  Second there needs to be some user interface to choose which should be clipped.  Your suggestion about having a toggle to clip only surfaces is user interface.  I agree the Chimera 1 per-model clipping user interface is a pain and we should do something more usable in ChimeraX.

[Tom Goddard]

I added a "clip model" command that allows turning off clipping for specified models (e.g. "clip model #!1 off"). It only effects scene clip planes (ones that rotate with the model), not the camera near / far clip planes.

The tricky part of this was get mouse selection to continue to work on parts of a model that would normally be clipped. I did it for ctrl-click but not for drag select. I can make drag select work but ran out of time today. It is quite possible that I broke picking in some scenarios, dozens of files got changed, and I was not able to thoroughly test everything.

[Tom Goddard]

Made drag select on clip disabled models work.