Remember previous clip plane positions

[rjr27@…]

There's a "clip off" command, but no obvious way to turn clipping planes back on with the original defaults.

[pett]

Reported by Randy Read

[Elaine Meng]

Hi Randy,
There aren’t “initial defaults” for clipping.  If you wanted clipping in the same positions you had before, you would just have to use the same process as you did before to get there.  The previous positions aren’t remembered when you turn clipping off.  
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>

Maybe clipping got turned on as a side effect of using “view” on specific items.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial>

We do appreciate feedback, but you could try asking about some things on the chimerax-users@cgl.ucsf.edu mailing list rather than assuming that they’re all bugs.  You can also make suggestions on this list.

[rjr27@…]

Hi Elaine,

I hadn’t actually adjusted the clipping planes at this point, so they were in whatever positions they got to by being initialized — maybe they’re changed by recentering or by switching between ortho and mono modes, but I didn’t do anything explicit to them. 

Basically, I was trying things I hadn’t tried before as part of making a picture, and I found the clipping of a (90% transparent) surface to be distracting.  I used the command “clip off”, didn’t like the result in terms of the accompanying changes to depth cueing, and was surprised not to be able to undo it!  At that point, Tristan Croll suggested that I should go into side view to adjust them manually, which worked very well (apart from the camera movement problem I also noted!)

However, I can appreciate that remembering everything about a previous state could be a daunting and unrewarding task.

Best wishes,

Randy

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research     Tel: +44 1223 336500
The Keith Peters Building                               Fax: +44 1223 336827
Hills Road                                                       E-mail: rjr27@cam.ac.uk
Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk

[Elaine Meng]

Hi Randy,
Clipping is off by default, so I don’t know how it got turned on in your case; as far as I understood it, there is no initial default state per se, but the different ways it could have been turned on may use various rules for where the planes start out.  Besides the clip command, the ways I can think of that might turn on clipping are the view command and using certain mouse modes.  In the latter case, the exact positioning may depend also on what was displayed and the positions of the models at the time and where in the window you clicked.  I guess the only real solution would be to remember where they were when turned off, but as the only nonprogrammer on the team, I don’t know how feasible that might be.
Best,
Elaine

[Tom Goddard]

You could turn on clip planes with the "clip" command or the clip mouse modes (translate or rotate). In either case it initially makes a plane passing through the center of the bounding box of the displayed models. If you turn off clipping (command "clip off") then later enable clipping again it doesn't remember your previous plane positions -- instead it will once again place the plane perpendicular to the view direction through the center of the bounding box. If you were showing the exact same scene then the center point should be the same and you should have obtained the same clip position. If you were using clip planes fixed in the scene (rather than fixed to the screen), then if you rotated the view between the first and second time you enabled clip planes, then the plane would be oriented differently. Not sure if that is what you observed.

Currently the clipping does not remember where the planes were when you turned them off. It could remember the plane locations and reuse them. Sometimes that is what is needed. But I suspect most often the user wants to establish new clip plane positions based on their current view. Various bad outcomes can result from restoring past clip plane positions -- for instance I could have hidden the model where I originally showed clip planes, shown another model positioned differently, and now I enable clip planes and sometimes nothing is clipped or everything is clipped. We could add options to the clip command that allow using the last clip positions or new positions through a center point. But I suspect almost no-one would ever discover or use those options, so it is better to think about how to make the best default behavior. I don't have an idea about how to improve the current behavior.

[rjr27@…]

Hi Elaine,

Thanks!  It's good to have an explanation.  Now that I'm a slightly-less-novice user, I'll go to the side view whenever I want to do something specific with clipping, and that works pretty well and intuitively (at least in "camera mono" mode, which I may learn to appreciate more).  It probably happened when I used a "view" command to center on the residue where I wanted to illustrate the effect of a mutation.

As the PI of a team that also develops software for academic researchers, I have to say that I'm incredibly impressed with the responsiveness of the ChimeraX team to bug reports and feature requests!  We try but we're not nearly so well organised.

Best wishes,

Randy


------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research     Tel: + 44 1223 336500
The Keith Peters Building                               Fax: + 44 1223 336827
Hills Road                                                       E-mail: rjr27@cam.ac.uk
Cambridge CB2 0XY, U.K.                             www-structmed.cimr.cam.ac.uk