<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 Gustavo,<div class=""><br class=""></div><div class=""> Glad you noticed the smoothness of the surface. I made it smoother than the default. The surface came from the molmap command which computes a density map from the atomic model. That command uses a density map grid spacing of 1/3 the requested resolution by default, but I specified an extra option that used a grid spacing 1/8 of the resolution:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 2gbp</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>molmap #1 8 gridSpacing 1</div><div class=""><br class=""></div><div class="">Also if you are doing this with a big molecule (100,000 atoms) the density map created may be very large and may be shown subsampled so the surface looks coarser. Make sure to set the "step" to 1 in the Volume Viewer panel so that it uses the full resolution of the computed map instead of step 2 which would use only every other grid point.</div><div class=""><br class=""></div><div class=""> One more pro tip about that image composition example. It only worked nicely because the atomic structure was completely behind the surface, so I could layer the surface on top. If part of the atomic model was behind and part in front (for example with a cryoEM map surface), then the layering would not work well -- the composite image would have the surface in front everywhere. Elaine's selection highlight approach can handle that situation with correct occlusions but the edging is not as nice as silhouettes.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 31, 2021, at 1:00 PM, de Miranda Seabra, Gustavo <<a href="mailto:seabra@cop.ufl.edu" class="">seabra@cop.ufl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt; background-color: rgb(255, 255, 255);" class="">Hi Tom,</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt; background-color: rgb(255, 255, 255);" class="">This looks beautiful! <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt;" class="">Just one tangential question: How do you get such a smooth surface? Can you share the exact commands you gave?</span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt; background-color: rgb(255, 255, 255);" class="">Thanks!</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">--</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><b class="">Gustavo Seabra</b></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Assistant Scientist</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Center for Natural Products, Drug Discovery and Development (CNPD3)</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Department of Medicinal Chemistry</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">College of Pharmacy</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">University of Florida, Gainesville, FL, USA</div></div></div></div><div id="appendonsend" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 722.25px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" class="">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, March 30, 2021 8:55 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Andre LB Ambrosio <<a href="mailto:andre@ifsc.usp.br" class="">andre@ifsc.usp.br</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] Displaying silhouette around specific visual elements</font><div class=""> </div></div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; line-break: after-white-space;"><div class=""><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(250, 70, 22);" class=""><b class="">[External Email]</b></span></div><table border="0" cellspacing="0" cellpadding="0" align="left" width="100%" class=""></table><div class="">Hi Andre,<div class=""><br class=""></div><div class=""> If you are willing to go to a little trouble you can get silhouettes on an atomic model beneath a transparent surface that has no silhouettes. You first save an image of the atomic model with silhouettes with no surface, then save an image of the transparent surface with no atomic model and no silhouettes, then overlay the second image on the first in a photo editor like Gimp. Below is Elaine's example done this way. The command to save the surface image with transparency for overlaying is "save transpsurf.png transparentBackground true".</div><div class=""><br class=""></div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>Tom</div><div class=""><br class=""></div><div class="">Overlay of two images.</div><div class=""><img id="x_CECDC4D8-9293-4008-8CC5-3AF7F18285A6" class="" data-outlook-trace="F:1|T:1" apple-inline="yes" width="663" height="491" src="cid:DA1865B9-D543-4DD4-B27A-78FA451CF176"></div><div class=""><br class=""></div><div class="">Atomic model image</div><div class=""><br class=""></div><div class=""><img id="x_8AB40544-8105-4E3F-8286-14954F2D7C41" class="" data-outlook-trace="F:1|T:1" apple-inline="yes" width="663" height="491" src="cid:A3784594-8314-4BA2-8AFD-7DFAE86E0210"></div><div class="">Transparent surface image</div><div class=""><img id="x_825BCD4B-A315-4054-8562-C963FC28C364" class="" data-outlook-trace="F:1|T:1" apple-inline="yes" width="663" height="491" src="cid:AFB63E41-44E4-4F75-9C07-A217A23B38AC"><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Mar 30, 2021, at 3:11 PM, Andre LB Ambrosio <<a href="mailto:andre@ifsc.usp.br" class="">andre@ifsc.usp.br</a>> wrote:</div><br class="x_Apple-interchange-newline"><div class=""><div dir="ltr" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><div class="">Dear Elaine, that is excellent! It is the visual effect I was looking for indeed.</div><div class="">Thank you very much for this and thank you Tom for the very detailed response and for the feature request ticket.</div><div class="">Andre.<br class=""></div></div><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><div class="x_gmail_quote" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><div dir="ltr" class="x_gmail_attr">Em ter., 30 de mar. de 2021 às 15:59, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> escreveu:<br class=""></div><blockquote class="x_gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class="">Hi Andre,<div class="">Sometimes you can approximately "fake" this effect by using the selection outline. It is not the same, however, as silhouettes; it will only go around the outside perimeter of the selected item(s). For example, if I have a molecule inside a map surface, I can make the surface transparent, select the atomic structure, and make the selection outline color black etc. as in these commands, resulting in the appearance in the attached image.<div class=""><br class=""></div><div class="">open 2gbp<br class="">molmap protein 8<br class="">trans 70<br class="">view<br class="">set bgColor white<br class="">select @*<br class="">graphics selection color black<br class=""><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><img id="x_gmail-m_8106015797148862846D1B49E5A-D6C7-4A09-9A8C-5A426849C9EF" class="" data-outlook-trace="F:1|T:1" apple-inline="yes" width="477" height="297" src="cid:178852b12d979c999e31"><br class=""><br class=""></div><br class=""><blockquote type="cite" class="">On Mar 25, 2021, at 8:23 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank" class="">goddard@sonic.net</a>> wrote:<br class=""><br class="">Hi Andre,<br class=""><br class=""> It is not currently possible to display silhouettes on some models and not others.<br class=""><br class=""> Several people have wanted this but I think it is complex to achieve. The silhouettes show boundaries where the depth in the entire scene changes abruptly. In order to have per-model silhouettes the ChimeraX GPU shader programs would need to compute an additional depth buffer separately for each model. Also the silhouette edges are not currently drawn at a specific depth. If per-model silhouettes were supported a stick model with silhouettes beneath a transparent surface needs to draw the silhouettes under the transparent surface so knowing the depth of the silhouette edge becomes important. When not using silhouettes the shader programs need to not compute the extra per-model depth buffers otherwise it would slow down rendering even when not being used. Adding these additional complexities to already complex graphics rendering shader programs have so far made this feature out of reach for our one graphics rendering developer (me).<br class=""><br class=""> I made a feature request for per-model silhouette edges and perhaps in the future we will find a simpler way to implement it that makes it feasible.<br class=""><br class=""><span class="" style="white-space: pre-wrap;"></span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac_ChimeraX_ticket_4420&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=IFgzc8_Vdkz-B7UF2uxuBCj87hyWuUEjWI2N297ETz4&m=buIaGFiuOEg93LpD7JBCYgWU_w9PFNqzQcrtEu3dwS4&s=4rNagowyowqf-kDt4FSpoXKb-pTc5iJJptB8I4YexpU&e=" target="_blank" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4420</a><br class=""><br class=""> Tom<br class=""><br class=""><blockquote type="cite" class="">On Mar 25, 2021, at 10:09 PM, Andre LB Ambrosio <<a href="mailto:andre@ifsc.usp.br" target="_blank" class="">andre@ifsc.usp.br</a>> wrote:<br class=""><br class="">Dear all,<br class=""><br class="">I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them.<br class="">Many thanks in advance, <br class=""><br class="">Andre<br class="">_</blockquote></blockquote></div></div></div></div></blockquote></div><br clear="all" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; float: none; display: inline !important;">--<span class="x_Apple-converted-space"> </span></span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><div dir="ltr" class="x_gmail_signature" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><div dir="ltr" class=""><div class="">Andre LB Ambrosio</div><div class="">Associate Professor, IFSC/USP - Brazil</div><div class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ifsc.usp.br_alba&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=IFgzc8_Vdkz-B7UF2uxuBCj87hyWuUEjWI2N297ETz4&m=buIaGFiuOEg93LpD7JBCYgWU_w9PFNqzQcrtEu3dwS4&s=ySFDlzFgm5R9qi6-4q_NIK-FlZAlewimOtx8sOwInfA&e=" target="_blank" class="">www.ifsc.usp.br/alba</a><br class=""></div></div></div><span class="" style="font-family: Helvetica; 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