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@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@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