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

Oliver Clarke olibclarke at gmail.com
Wed Apr 27 10:25:45 PDT 2016

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

mclip # match nearfar
turn y 90
adjust clip planes
take image1
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!


On Wed, Apr 27, 2016 at 12:43 PM, Elaine Meng <meng at cgl.ucsf.edu> 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>
> 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 <olibclarke at gmail.com> 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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