<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 Chuck,<div class=""><br class=""></div><div class=""> You can make transparent surfaces cast ambient shadows with command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>material transparentCastShadows true</div><div class=""><br class=""></div><div class="">The default is that transparent surfaces do not cast shadows because usually that gives a better result in the common case where most of the structure is inside the transparent surface and the point of making it transparent is to see inside. But if you cast ambient shadows from the transparent surface then the structure inside will be entirely black and hard to see. The shadow casting is not sophisticated enough to partially shadow, so a transparent surface will cast a shadow as if it is 100% opaque. To allow some light through would require ray-tracing which is an entirely different technology for drawing graphics than what ChimeraX uses. Only with the latest graphics high-end graphics cards (e.g. Nvidia RTX 2080) has raytracing become possible at interactive speeds.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 31, 2019, at 9:53 AM, Sindelar, Charles <<a href="mailto:charles.sindelar@yale.edu" class="">charles.sindelar@yale.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">PS: one more note is that after I destroy my nice rendering in ChimeraX v0.6 by unshowing and showing the PDB model, I can restore it by the following sequence:<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><ol start="1" type="1" style="margin-bottom: 0in; margin-top: 0in;" class=""><li class="MsoListParagraph" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;"><span style="font-size: 11pt;" class="">Adjust map opacity to 100%<o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;"><span style="font-size: 11pt;" class="">Unshow and reshow anything (ambient lighting returns)<o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;"><span style="font-size: 11pt;" class="">Adjust map opacity to 80% (ambient lighting stays)<o:p class=""></o:p></span></li></ol><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="" class="">"Sindelar, Charles" <<a href="mailto:charles.sindelar@yale.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">charles.sindelar@yale.edu</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Saturday, August 31, 2019 at 12:44 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>semitransparent volumes with ambient occlusion<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">Here is a little request.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off!<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">I sure would like to have this option! I guess there must be some reason it is disabled? <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">Best, Chuck Sindelar<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">Opaque map + PDB (ChimX v0.6)<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">(pretty but the PDB is obscured)<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image001.png@01D55FFB.1378EDE0"><image001.png></span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">After adjust to 80% map opacity (ChimX v0.6)<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">(pretty!)<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image002.png@01D55FFB.1378EDE0"><image002.png></span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">After unshow/show PDB model (ChimX v0.6)<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">(argh!)<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image003.png@01D55FFB.1378EDE0"><image003.png></span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; 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