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<p class="MsoNormal">Hi Tom, this is exactly what I was looking for! I see the drawbacks of it, but nevertheless it’s nice to have this option. Greetings from New Haven – Chuck<o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Tom Goddard <goddard@sonic.net><br>
<b>Date: </b>Tuesday, September 3, 2019 at 12:18 PM<br>
<b>To: </b>"Sindelar, Charles" <charles.sindelar@yale.edu><br>
<b>Cc: </b>"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] semitransparent volumes with ambient occlusion<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Chuck, <o:p></o:p></p>
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<p class="MsoNormal"> You can make transparent surfaces cast ambient shadows with command<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">material transparentCastShadows true<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Aug 31, 2019, at 9:53 AM, Sindelar, Charles <<a href="mailto:charles.sindelar@yale.edu">charles.sindelar@yale.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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:<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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Adjust map opacity to 100%<span style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-top:0in;margin-bottom:0in;margin-bottom:.0001pt;mso-list:l0 level1 lfo1">
Unshow and reshow anything (ambient lighting returns)<span style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-top:0in;margin-bottom:0in;margin-bottom:.0001pt;mso-list:l0 level1 lfo1">
Adjust map opacity to 80% (ambient lighting stays)<span style="font-size:12.0pt"><o:p></o:p></span></li></ol>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">"Sindelar, Charles" <<a href="mailto:charles.sindelar@yale.edu"><span style="color:#954F72">charles.sindelar@yale.edu</span></a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Saturday, August 31, 2019 at 12:44 PM<br>
<b>To:<span class="apple-converted-space"> </span></b>"<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style="color:#954F72">chimerax-users@cgl.ucsf.edu</span></a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style="color:#954F72">chimerax-users@cgl.ucsf.edu</span></a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>semitransparent volumes with ambient occlusion<o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Here is a little request.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">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></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">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></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">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></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">I sure would like to have this option! I guess there must be some reason it is disabled? <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Best, Chuck Sindelar<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Opaque map + PDB (ChimX v0.6)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">(pretty but the PDB is obscured)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><image001.png><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">After adjust to 80% map opacity (ChimX v0.6)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">(pretty!)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><image002.png><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">After unshow/show PDB model (ChimX v0.6)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">(argh!)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><image003.png><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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