<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Abba,<div class="">Here are some ideas, which are not exactly what you describe but may accomplish your goals. See the images attached below.</div><div class=""><br class=""></div><div class="">(1) use per-model clipping plane in “slab” mode, which can show a slice of any thickness at any angle</div><div class=""><br class=""></div><div class="">(2) open the same structure again, but not clipped, and make it ghostly, like 80% transparent</div><div class=""><br class=""></div><div class="">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:</div><div class="">- how to rotate and translate this slab of visibility on the protein</div><div class="">- 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)</div><div class="">- remember to turn off “adjust clipping with mouse” in order to use those mouse buttons as you normally do to translate/zoom the view</div><div class=""><br class=""></div><div class="">So I made some example images with 2gbp, with explanation of how I got them:</div><div class=""><br class=""></div><div class="">open 2gbp</div><div class="">ribbon; show ligand; repr sphere ligand</div><div class="">[ 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 ]</div><div class="">open 2gbp</div><div class="">mcopy #0 #1 settings a</div><div class="">transp 80 #1</div><div class="">set bg_color white</div><div class="">[you can do more positioning/rotation of the slab and adjusting its thickness ]</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="3A0B83AE-BE18-4709-89AC-C67233190D6B" src="cid:3E1E1DF7-7B17-420B-AFD8-83715E056F17@compbio.ucsf.edu" class=""></div><div class="">set silhouette</div><div class="">setattr m silhouette false #1</div><div class=""><img apple-inline="yes" id="08D1CE9D-95DE-4085-9A3B-5972AA9E81E2" src="cid:517B5157-D8EF-4309-9F27-6CEE9CE02DD2@compbio.ucsf.edu" class=""></div><div class="">~set silhouette; ~ribbon; surf</div><div class="">transp 80 #1</div><div class="">[… no visible change because model #0 surface is not clipped, only the atoms/ribbon …]</div><div class="">[ 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 ]</div><div class="">color green,a C</div><div class="">repr bs ligand</div><div class="">[ you can hide/show the ghostly one using the “S” checkbox in the Model Panel]</div><div class=""><img apple-inline="yes" id="6AF837CE-B6A3-4ABA-9FF0-3DF0BC8F223A" src="cid:A7ED958E-640C-46F5-9D7B-BD546B65EA36@compbio.ucsf.edu" class=""></div><div class=""><img apple-inline="yes" id="7E4D5D89-5D9C-4E94-AA82-A31FA2776BDF" src="cid:0ADF2BF8-BF0D-4847-97F0-E6949EAA317B@compbio.ucsf.edu" class=""></div><div class=""><img apple-inline="yes" id="183FCBA9-83A4-4C92-A7E9-BD08C31A4B9D" src="cid:A03A5DBF-1E68-45CB-A4CB-99671B7761B0@compbio.ucsf.edu" class=""></div><div class="">There are a lot of possibilities, I just tried to give you the flavor of it.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">----------<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""></div><br class=""><blockquote type="cite" class="">On Mar 30, 2017, at 2:38 PM, Abba E Leffler <<a href="mailto:ael355@nyu.edu" class="">ael355@nyu.edu</a>> wrote:<br class=""><br class="">Dear All:<br class=""><br class="">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.<br class=""><br class=""><br class="">Is there a way to get the heights of the clipping planes, and then draw planes representing them?<br class=""><br class="">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?<br class=""><br class="">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.<br class=""><br class="">Thank you for your help<br class=""></blockquote><br class=""></div></body></html>