[Chimera-users] Define plane or planes matched to hither or yon clip planes

Tom Goddard goddard at sonic.net
Wed Apr 27 11:00:54 PDT 2016

Hi Oliver,

  One more step you probably want when showing clip plane positions in a side view is to use orthographic projection (command “set projection orthographic”, then to get back “set projection perspective”).  The Chimera side view dialog uses orthographic projection.  This makes the image projected exactly perpendicular to the screen so that the clip line really is the dividing line between what is and what is not clipped.

  I’m curious what kind of image you will composite from the two side images, one with per-model clip planes and one without clip planes.  Will you fade out the clipped away part (the unclipped image) then overlay the two?  Then draw in clip lines in a paint program?  In Chimera I think it would be pretty easy to make a shortcut that replaces near/far clip planes with per-model clip planes, adds two rectangular slabs, animates a rotation by 90 degees to show an edge on view, then unclips so you can see the models outside the clip planes, with rectangular slabs now viewed edge-on to show the boundary between clipped and unclipped.  Then the same shortcut could reverse all those steps to get you back to the original view.  In ChimeraX we could be even fancier and have the part outside the clip planes be faded.


> On Apr 27, 2016, at 10:25 AM, Oliver Clarke  wrote:
> Hi Elaine, actually this works pretty well, thanks! Because if you supply # to mclip it will clip all models, so that makes it easier than I had been thinking:
> mclip # match nearfar
> turn y 90
> adjust clip planes
> take image1
> ~mclip
> take image2
> then image1 and image2 can be overlayed in illustrator or equivalent to generate the kind of image I want. Thanks for the tip!
> Cheers,
> Oli.
> On Wed, Apr 27, 2016 at 12:43 PM, Elaine Meng  wrote:
> Hi Oli,
> The closest thing I can think of is that the per-model clipping command has an option to put the front and back of the slab at the hither and yon planes.  It’s “mclip” command with option “match nearfar” … but as you said, it is cumbersome to repeat for multiple models before turning everything 90 degrees.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html>>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Apr 27, 2016, at 8:25 AM, Oliver Clarke wrote:
> > Hi,
> > I often encounter cases where I am showing a slab of density or model (or both), clipped using the global clip planes, and would like to show the viewer a thumbnail illustrating the position of these clip planes from an orientation orthogonal to the viewing direction (similar to what is shown in side view), to give context.
> >
> > Is there any way to define either two planes, one matched to the current yon and one matched to the global hither, or one thick plane with the thickness defined such that one side matches hither and the other yon?
> >
> > Alternatively I guess I can do this using the model-specific clip planes, but that's a little cumbersome to do when many models/maps are involved.
> > Cheers,
> > Oli
> >
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