<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="">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><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>perframe “vdwdens 5.1; vdwdens 5”</div><div class=""><br class=""></div><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><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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><div class=""><br class=""></div></div>
</div>
<div><br class=""><blockquote type="cite" class=""><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><br class="Apple-interchange-newline"><div class=""><div class="">Hi Brian,<br class="">This is not a direct answer to your question, but alternatives to showing VDW dots are: <br class=""><br class="">(A) show sphere representation (VDW spheres) instead of stick representation of atoms<br class=""><br class="">(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=""><br class="">surftrans 75<br class="">surftrans 0<br class="">surfrep mesh<br class=""><br class="">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=""><br class="">Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds.<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">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=""><br class=""><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=""><br class="">Hello,<br class=""><br class="">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=""><br class="">Thanks,<br class="">Brian<br class=""><br class="">---<br class="">Brian E. Coggins, Ph.D.<br class="">Assistant Research Professor of Biochemistry<br class="">Duke University, Durham, NC<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>