<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Glad it did what you needed!<div class=""><br class=""></div><div class="">—Eric</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 24, 2019, at 11:29 AM, Brian E Coggins <<a href="mailto:bec2@duke.edu" class="">bec2@duke.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Eric,
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<div class="">Hack or not, this does the job perfectly! Many thanks.</div>
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<div class="">Brian</div>
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<div class="">On Jan 23, 2019, at 6:36 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div>
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Hi Brian,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>It seems the vdw command caches the computed surface points and that therefore various tricks with ~vdw/vdw don’t update the surface. However changing the dot density does clear the
cache and cause a recomputation, so you can use this awful hack to get the vdw surface to update as you adjust torsions:</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>perframe “vdwdens 5.1; vdwdens 5”</div>
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<div class="">Every frame, the density will be changed to 5.1 and then back to the (default) 5. You might want to use different numbers. I prefer not to be “credited” with this idea. :-)</div>
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>not Eric Pettersen</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>not from the UCSF Computer Graphics Lab</div>
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<div class="">On Jan 23, 2019, at 3:14 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
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<div class="">Hi Brian,<br class="">
This is not a direct answer to your question, but alternatives to showing VDW dots are:
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(A) show sphere representation (VDW spheres) instead of stick representation of atoms<br class="">
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(B) show molecular surface, which will update as bonds are rotated. You could make it transparent and/or show it as mesh, e.g. commands:<br class="">
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surftrans 75<br class="">
surftrans 0<br class="">
surfrep mesh<br class="">
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There is also a “dot” style (as opposed to mesh and solid) but then you’d want to crank up the vertex density to put the dots closer together… e.g. select the surface with Ctrl-click and then use the Selection Inspector (open by clicking green magnifying glass
icon), inspect: MSMS surface, increase “vertex density” and maybe dot size.<br class="">
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Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds.<br class="">
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I hope this helps,<br class="">
Elaine<br class="">
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Elaine C. Meng, Ph.D.<br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
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<blockquote type="cite" class="">On Jan 23, 2019, at 1:29 PM, Brian E Coggins <<a href="mailto:bec2@duke.edu" class="">bec2@duke.edu</a>> wrote:<br class="">
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Hello,<br class="">
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If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure
changes?<br class="">
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Thanks,<br class="">
Brian<br class="">
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Brian E. Coggins, Ph.D.<br class="">
Assistant Research Professor of Biochemistry<br class="">
Duke University, Durham, NC<br class="">
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<div class="">Brian E. Coggins, Ph.D.</div>
<div class="">Assistant Research Professor of Biochemistry</div>
<div class="">Duke University, Durham, NC</div>
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