Clip mouse mode control of scene, screen and per-model clip planes

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-05)
Description
Hi,

Another minor feature request. The "clip" right mouse mode seems to act the same as per model clipping planes in Chimera - that is, when the view is rotated, the clip plane rotates with the model. This is really useful in some cases (e.g. slicing through a molecular surface to expose a ligand binding pocket), but in many cases (e.g examining EM map in conjunction with model) it is more useful to manipulate the global clip planes, as one can do with side view. Would it be possible to add a right mouse mode for this case? So that then there would be two - "Global clip" and "per model clip" I guess? Also, is there a way to assign Z-translation to a trackpad gesture? E.g. in Chimera I have this assigned to Ctrl-right-click-drag, so I can quickly slab through a map.

Cheers
Oli

PS ChimeraX is looking much more polished and getting better every day, using it more and more!

Log:
UCSF ChimeraX version: 0.9 (2019-06-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1bl8 format mmCIF fromDatabase pdb

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> camera ortho

> toolshed show Toolbar

> ui mousemode rightMode "crop volume"

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ~clip

> ui mousemode rightMode zone

> zone /B:99

> zone /B:99 residueDistance 6.6 labelDistance 5.28 surfaceDistance 10.6

> zone /B:99 residueDistance 10.1 labelDistance 8.08 surfaceDistance 16.2

> zone /B:99 residueDistance 13.2 labelDistance 10.5 surfaceDistance 21.1

> zone /B:99 residueDistance 10.1 labelDistance 8.08 surfaceDistance 16.2

> zone /D:95

> zone /B:39

> zone /A:38

> zone /C:34

> zone /D:98

> zone /B:39

> zone label false

> zone clear

> zone clear

> zone /A:30

> zone label false

> zone clear

> zone clear

> zone clear

> zone /B:34

> zone label false

> zone clear

> zone clear

> zone /D:33

> zone label false

> zone /D:38

> zone /A:101

> zone label false

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> ~clip

> ui mousemode rightMode "move planes"

> toolshed show "Side View"

> ui mousemode rightMode translate

> help help:user/tools/Toolbar.html




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

ChimeraX does not have per-model clipping yet. It has clip planes fixed in the scene and clip planes relative to the view direction.

The clip mouse mode allows you to move near and far clip planes together by holding the shift key down. Or you can move just the rear plane by holding the alt key down.

The clip mouse mode doesn't currently let you control whether it uses scene clip planes or view clip planes. I think having two separate modes for that is going to be confusing. And when we add per-model clipping would we use a third mouse mode to control those?

Currently if view clip planes are enabled with say the clip command, then the mouse mode uses view clip planes. But if no clip planes are shown, then the clip mouse mode will make scene clip planes. We could potentially have a preference setting so the clip mouse mode could always make view clip planes.

Another idea is that enabling the clip mouse mode will show a small panel in the right column of panels where you choose which kind of clip planes you want to create or move. Such a panel could also allow rotating scene clip planes. Currently rotating is a separate mouse mode.

[olibclarke@…]

Hi Tom

I would *much* prefer if clipping relative to the view direction was the default - I find the current behavior confusing coming from chimera, where all clip planes are relative to the view except for the per model clip planes (which again are useful, but only in niche cases in my experience).

Perhaps clipping fixed in the scene could be called cropping, as it seems to be for volumes?

If anything I would definitely prefer defaulting to “view” clip planes. I can’t seem to find a way to use the clip mouse mode with the “view” clip mode actually - if I don’t have clip planes on (e.g. running ~clip just before use), it creates “scene” clip planes, and if I already have “scene” clip planes it just moves them.

Cheers
Oli

[goddard@…]

If you use command "clip near 0" to enable a view clip plane then use the clip mouse mode it moves the view clip planes and does not create scene clip planes.

Clip planes need more work including what the defaults should be.

[Tom Goddard]

I added a preference setting under the Clipping tab "Mouse clip enables [scene planes / screen planes]". This controls whether the clip plane it creates when you first click rotates with the scene or remains parallel to the screen. The default is scene, but if you more often need screen you can change that preference and save the setting for future sessions.

This does not address the problem of how you control scene and screen and in the future per-model planes with the mouse. I think a future solution will be to provide a panel to configure the clip mouse mode (which might also control rotating scene clip planes, reducing the current two clip modes (translate and rotate) to one). This improvement is not likely to get any attention for a long time given our many other higher priorities.

[olibclarke@…]

Thanks Tom - this is already a big improvement1

Cheers
Oli