<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Scott,<div><br></div><div> I made a ChimeraX recipe web page to show this transparency and shadows trick.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://rbvi.github.io/chimerax-recipes/shadows/shadows.html">https://rbvi.github.io/chimerax-recipes/shadows/shadows.html</a></div><div><br></div><div> That's amazing Esther refound it in that long fitting video.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br><div><br><blockquote type="cite"><div>On Feb 10, 2023, at 12:23 PM, Scott Stagg <sstagg@fsu.edu> wrote:</div><br class="Apple-interchange-newline"><div>
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Thanks, Tom. That’s exactly what I was looking for! Esther Bullit found the video. It’s this one
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<a rel="nofollow" href="https://www.youtube.com/watch?v=v3jI43YJQMg" style="text-decoration: none" draggable="false"><font color="#272727" style="">Fitting an atomic model in an electron microscopy map with ChimeraX</font></a></div>
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<a rel="nofollow" href="https://www.youtube.com/watch?v=v3jI43YJQMg" style="text-decoration: none" draggable="false"><font color="#808080" style="">youtube.com</font></a></div>
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<div>Scott</div>
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<div>On Feb 10, 2023, at 3:09 PM, Tom Goddard <goddard@sonic.net> wrote:</div>
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Hi Scott,
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<div> I'm not sure what video that is in. But there is some obscure ChimeraX magic involved. If you use the "soft" lighting (shadows cast from all directions) with a transparent surface it looks horrible because transparent surfaces by default don't cast
shadows in ChimeraX. The reason for that default is often you are showing a molecule inside a transparent surface and then the molecule is dark (black actually) and hard to see. Because the transparent surface doesn't cast shadows it does not shadow itself
so you don't get any of the darkened cavities that help 3D appearance. To make transparent surface cast shadows use ChimeraX command</div>
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<div><span class="Apple-tab-span" style="white-space:pre"></span>material transparentCastShadows true</div>
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<div>If you have an atomic structure (#2) inside the surface it will look black (shadowed), but you can tell it not to accept shadows</div>
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<div><span class="Apple-tab-span" style="white-space:pre"></span>lighting model #2 multishadow false</div>
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<div>The model inside can look pretty horrible and flat with soft lighting and you might try full lighting that adds a spot light, and also use silhouette edges.</div>
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<div> Here is an example of all these tricks.</div>
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<div><span class="Apple-tab-span" style="white-space:pre"></span>open 1080 from emdb</div>
<div><span class="Apple-tab-span" style="white-space: pre;"></span>light soft</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>volume level 0.6</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>open 1grl</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>preset cylinders</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>fitmap #2 in #1</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>transparency #1 80</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>material transparentCastShadows true</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>lighting model #2 multishadow false</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>graphics silhouettes true</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>set bgColor white</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>light full</div>
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<div>Thanks for asking!</div>
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<div> Tom</div>
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<div>Opaque map, and transparent map, and transparent map with shadows with soft lighting.</div>
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<div>Atomic model is dark inside transparent map casting shadows. Can make atomic model not accept shadows. "Full" lighting instead of soft can make the atomic look less flat.</div>
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<div>On Feb 10, 2023, at 6:48 AM, Scott Stagg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</div>
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Hi everybody,
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<div>I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that
you typed in the command line. Do you know what I’m talking about?</div>
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<div>Thanks,</div>
<div>Scott</div>
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Scott Stagg<br>
Professor<span class="Apple-tab-span" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: pre; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">
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Institute of Molecular Biophysics<br>
Department of Biological Sciences</div>
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Florida State University<br>
Tallahassee, FL 32306-4380<br>
w: 850-645-7872<br>
f: 850-644-7244<br>
sstagg@fsu.edu<br>
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