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

Tom Goddard goddard at sonic.net
Wed Apr 27 11:03:41 PDT 2016

One more question, why not just take a screen snapshot of the side view dialog?  I guess you want more control of what it looks like (e.g. no view bounding lines).  Could you explain or show an example image of exactly what you are aiming for?


> 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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