<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=""><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">Hi David,</p><div class=""><font size="2" class="">ChimeraX does not have the flat transparency option. I have made a feature request for it</font></div><div class=""><font size="2" class=""><br class=""></font></div><div class=""><font size="2" class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5294" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5294</a></font></div><div class=""><font size="2" class=""><br class=""></font></div><div class=""><font size="2" class="">We plan to freeze the ChimeraX code in preparation for the ChimeraX 1.3 release this week, so I will not add this right now, but it should be pretty easy to add.</font></div><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""> I see you are trying to use transparency to achieve fading of the ribbon. So you don't want the angle dependent transparency where edge on transparent surfaces appear opaque, giving a more 3-dimensional appearance. You just want it all equally faded.<br class=""></p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""> If you want to edit your ChimeraX distribution you can make it use flat transparency. The file to edit is (on Mac)</p><blockquote style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""><p class="">ChimeraX-1.2.5.app/Contents/lib/python3.8/site-packages/chimerax/graphics/fragmentShader.txt<br class=""></p></blockquote><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">and you should add a "#" character in front of the following line using a text editor</p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));</p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">so it becomes<br class=""></p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""># a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));<br class=""></p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">This is the line in the graphics shader program that applies the angle dependent transparency. With this change, all transparency will be flat.</p><div class=""><font size="2" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Tom</font></div><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 27, 2021, at 12:43 PM, David William Kastner via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="WordSection1" style="page: WordSection1; 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;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">ChimeraX community,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I noticed that in ChimeraX, the “flat” transparency option that was present in Chimera has been either moved or renamed in ChimeraX. This setting made it so the transparency setting wasn’t overwhelming/distracting when focusing on details. In Chimera, it is accessed with Tools > Viewing controls > Effects > transparency > flat. Does anyone know how to achieve this effect in ChimeraX? I find the default ChimeraX transparency option to be disorienting when visualizing details. Here is a rendering comparing the two rendering styles with and without “flat” option. I look forward to your thoughts!<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0</a><o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">David<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="" class="">---<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="" class="">David Kastner</span></b><o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(95, 95, 95);" class="">Ph.D. student | Bioengineering</span><span style="" class=""><o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(95, 95, 95);" class="">MIT | Kulik Lab<o:p class=""></o:p></span></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(95, 95, 95);" class=""><a href="http://kastner.io/" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">kastner.io</a></span><o:p class=""></o:p></div></div><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; 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