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<p class="MsoNormal"><span style="font-size:11.0pt">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></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Adjust map opacity to 100%<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Unshow and reshow anything (ambient lighting returns)<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Adjust map opacity to 80% (ambient lighting stays)<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">"Sindelar, Charles" <charles.sindelar@yale.edu><br>
<b>Date: </b>Saturday, August 31, 2019 at 12:44 PM<br>
<b>To: </b>"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>semitransparent volumes with ambient occlusion<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal">Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward!
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Here is a little request.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I sure would like to have this option! I guess there must be some reason it is disabled?
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Best, Chuck Sindelar<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Opaque map + PDB (ChimX v0.6)<o:p></o:p></p>
<p class="MsoNormal">(pretty but the PDB is obscured)<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><img width="306" height="315" style="width:3.1875in;height:3.2812in" id="Picture_x0020_1" src="cid:image001.png@01D55FFB.1378EDE0" alt="cid:image001.png@01D55FF9.D8266CF0"><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">After adjust to 80% map opacity (ChimX v0.6)<o:p></o:p></p>
<p class="MsoNormal">(pretty!)<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><img width="306" height="315" style="width:3.1875in;height:3.2812in" id="Picture_x0020_3" src="cid:image002.png@01D55FFB.1378EDE0" alt="cid:image002.png@01D55FF9.D8266CF0"><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">After unshow/show PDB model (ChimX v0.6)<o:p></o:p></p>
<p class="MsoNormal">(argh!)<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><img width="306" height="315" style="width:3.1875in;height:3.2812in" id="Picture_x0020_5" src="cid:image003.png@01D55FFB.1378EDE0" alt="cid:image003.png@01D55FF9.D8266CF0"><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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