[Chimera-users] Get side-view model? Or, height of clipping planes?

Abba E Leffler ael355 at nyu.edu
Thu Mar 30 17:01:08 PDT 2017


That's perfect Elaine, thank you. I really appreciate your making the
images as well. It's very analogous to the system I am modeling. I will
play around with this and touch base if I have further questions.

Thanks again for taking the time.

On Thu, Mar 30, 2017 at 7:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Abba,
> Here are some ideas, which are not exactly what you describe but may
> accomplish your goals.  See the images attached below.
>
> (1) use per-model clipping plane in “slab” mode, which can show a slice of
> any thickness at any angle
>
> (2) open the same structure again, but not clipped, and make it ghostly,
> like 80% transparent
>
> Then you can either show the slice on its own, at any angle, or with the
> ghostly representation of the whole protein, again at any angle.  There are
> many options for display.  I wasn’t sure whether you were showing the
> atoms/ribbons of the protein or a surface, but it can be done either way.
> In per-model clipping, the main things to understand are:
> - how to rotate and translate this slab of visibility on the protein
> - that you can slice the surface of a protein without slicing its
> atoms/ribbons and vice versa (surface and atoms are two separate models,
> and per-model clipping is per model, as the name suggests)
> - remember to turn off “adjust clipping with mouse” in order to use those
> mouse buttons as you normally do to translate/zoom the view
>
> So I made some example images with 2gbp, with explanation of how I got
> them:
>
> open 2gbp
> ribbon; show ligand; repr sphere ligand
> [ then open Per-Model Clipping from under menu Tools… Depiction, enable
> clipping “2gbp (#0)” , turn on slab mode, turn on adjust with mouse, then
> change slab thickness and use mouse to position/rotate the slab to your
> liking ]
> open 2gbp
> mcopy #0 #1 settings a
> transp 80 #1
> set bg_color white
> [you can do more positioning/rotation of the slab and adjusting its
> thickness ]
>
> set silhouette
> setattr m silhouette false #1
> ~set silhouette; ~ribbon; surf
> transp 80 #1
> [… no visible change because model #0 surface is not clipped, only the
> atoms/ribbon …]
> [ now in Per-Model Clipping, enable clip “MSMS main surface of 2gbp #0”,
> slab mode, adjust with mouse the position and thickness of slab to your
> liking ]
> color green,a C
> repr bs ligand
> [ you can hide/show the ghostly one using the “S” checkbox in the Model
> Panel]
> There are a lot of possibilities, I just tried to give you the flavor of
> it.
>
> I hope this helps,
> 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 Mar 30, 2017, at 2:38 PM, Abba E Leffler <ael355 at nyu.edu> wrote:
>
> Dear All:
>
> I'm making a figure showing a ligand bound deeply in a cryptic pocket of a
> protein. To show it best, I've oriented the complex so that I am looking
> down directly on to it. Then, I adjust the hither and yon clipping planes
> to bracket the ligand so you get a cross-section through the protein
> containing the ligand and binding site.
>
>
> Is there a way to get the heights of the clipping planes, and then draw
> planes representing them?
>
> Better yet, can the image in the side view planning somehow be saved to
> high resolution with the yellow clipping planes indicated, but perhaps
> without the red field of view lines?
>
> Basically, for the figure I need some way of showing the viewer where the
> clipping planes are on the protein. This is critical because viewers need
> to know in a broad sense where the ligand is located.
>
> Thank you for your help
>
>
>
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