<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=""> To add the option requires that it be added to a command to set it, also it would need to be saved in sessions, and it would need to be documented in the manual — it would be about twice the work that was needed to make silhouettes show under transparent surfaces (which involved no user interface, session or documentation changes). It would be a small effort, maybe 4 hours work, but we have years of unimplemented feature requests, so it needs to be well justified.</div><div class=""><br class=""></div><div class=""> Let me know what you find as you make some new figures.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 30, 2019, at 3:04 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=""><div dir="ltr" class="">Hi Tom,<div class=""><br class=""></div><div class="">No - I'm not sure! I'm working on a couple myself at the moment, so I'll try with the new version :)</div><div class=""><br class=""></div><div class="">Either way, I understand your point - I was only asking in case it was only a small delta of effort on top of the work you'd just completed. I'm happy with and grateful for whatever features you & the team can deliver.</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Alexis</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 30, 2019 at 2:47 PM Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" 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="gmail-m_2084394139169539260Apple-tab-span" style="white-space:pre-wrap"> </span>Tom</div><div class=""><br class=""><div class=""><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" target="_blank" class="">a.rohou@gmail.com</a>> wrote:</div><br class="gmail-m_2084394139169539260Apple-interchange-newline"><div class="">
<div 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="gmail-m_2084394139169539260moz-cite-prefix">On 8/30/19 11:08 AM, Tom Goddard wrote:<br class="">
</div>
<blockquote type="cite" 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="gmail-m_2084394139169539260Apple-tab-span" style="white-space:pre-wrap"> </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="gmail-m_2084394139169539260cid:part1.E9EA8AB9.C3251B54@gmail.com" class=""><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" target="_blank" class="">yaohe@ucla.edu</a>> wrote:</div>
<br class="gmail-m_2084394139169539260Apple-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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