<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 Alexis,<div class=""><br class=""></div><div class=""> I’d prefer not to add super obscure options like turning off silhouette edges behind transparent surfaces. I think almost no one will use it and we have hundreds of other feature requests that I think would get use if we had time to implement them. Are you sure the figures you describe would not actually look better if both the outer transparent surface and inner opaque transmembrane surface were both silhouetted?</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 30, 2019, at 12:05 PM, Alexis Rohou <<a href="mailto:a.rohou@gmail.com" class="">a.rohou@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Hi Tom,</p><p class="">This is great! I'd often wished I could get silhouettes of opaque
models behind transparent surfaces.</p><p class="">However, there are also circumstances where the effect of having
silhouettes only around the outermost (front-most, I guess)
surface is very nice. A number of figures of membrane proteins
were published recently like that - the micelle is shown as a
low-resolution very-transparent blob with silhouette, and the
volume surface of the TM domain is shown inside it without
silhouette. Makes for a nice visual effect.</p><p class="">My question: could we perhaps have this new feature switchable
via the set command?</p><p class="">Cheers,<br class="">
Alexis<br class="">
</p>
<div class="moz-cite-prefix">On 8/30/19 11:08 AM, Tom Goddard wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:EFF67923-056D-447C-95DF-2C1286D18DBE@sonic.net" class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
Hi Yao,
<div class=""><br class="">
</div>
<div class=""> Yes ChimeraX is not showing silhouette edges on
molecules behind transparent surfaces. This is because ChimeraX
silhouette edges are drawn where the depth of the scene makes a
jump. The depth at a pixel is the depth of the front-most
object, so the transparent surface causes ChimeraX not to see
the depth of the molecule, hence no silhouette edge on the
molecule.</div>
<div class=""><br class="">
</div>
<div class=""> I just added some code that separately draws the
silhouette edges for opaque models and transparent models, so in
tonight’s ChimeraX daily build it will draw silhouettes on
molecules under transparent surfaces.</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>
<div class="">Here’s a picture Elaine Meng made illustrating the
problem you described, showing Chimera on left and ChimeraX on
right.</div>
<div class=""><br class="">
</div>
<div class=""><span id="cid:part1.E9EA8AB9.C3251B54@gmail.com"><Screen Shot 2019-08-30 at 9.33.44 AM.png></span></div>
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Aug 30, 2019, at 12:21 AM, YAO HE <<a href="mailto:yaohe@ucla.edu" class="" moz-do-not-send="true">yaohe@ucla.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi,
<div class=""><br class="">
</div>
<div class="">I am using ChimeraX now to show the
overlay between atomic model and transparent EM
densities. However, when I enable the silhouette
feature, only the transparent EM densities are
affected. I am wondering if it is possible to
also silhouette the atomic model inside. Just like "<span style="white-space: pre-wrap;" class="">setattr M silhouette true #3" in Chimera.</span></div>
<div class=""><span style="white-space: pre-wrap;" class="">
</span></div>
<div class=""><span style="white-space: pre-wrap;" class="">Best,</span></div>
<div class=""><span style="white-space: pre-wrap;" class="">Yao</span></div>
</div>
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