<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 David,<div class=""><br class=""></div><div class=""> It works for me when saving an image with a transparent background with white or black background with ChimeraX 1.2.5 or the daily build on macOS Big Sur. If it comes out blank for you with transparent background that sounds like a bug. Are you sure it is not just very faint? If it really is completely invisible you might want to use ChimeraX menu Help / Report a Bug... and attach an image without transparent background so I can replicate the problem.</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 Sep 27, 2021, at 4:31 PM, David William Kastner <<a href="mailto:kastner@mit.edu" class="">kastner@mit.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="">Thanks Tom!<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">This works perfectly for my needs. The figure looks great! If you want to add this to the ticket, the only problem I notice is that the “flat” transparency will render out blank when I select a PNG with a transparent background, but it works as expected with a white background. Thanks again.<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 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><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: blue; text-decoration: underline;" class="">kastner.io</a></span><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="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Monday, September 27, 2021 at 5:12 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>David William Kastner <<a href="mailto:kastner@mit.edu" class="">kastner@mit.edu</a>><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [chimerax-users] Flat transparency setting absent<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Oops! Actually the line needs to be preceded with // (two forward slashes) make it a comment not #. So it should look like<o:p class=""></o:p></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">// a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Tom<o:p class=""></o:p></div></div><div class=""><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=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Sep 27, 2021, at 1:48 PM, David William Kastner via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Tom,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you for the fast reply! Disabling the<span class="apple-converted-space"> </span><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">angle dependent transparency is exactly what I was looking for; however, when I commented the specified line in fragmentShader.txt on my Mac install of ChimeraX1.2.5, it throws an OpenGL error. The error is long, but the first line is:</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">('Shader compile failure (0): b"ERROR: 0:355: \'\' : Invalid Directive: a\\n"', [b'#version 330 core\n#define USE_LIGHTING 1\n#define USE_LIGHTING_NORMALS 1\n#define USE_DEPTH_CUE 1\n#define USE_SHIFT_AND_SCALE 1\n#define USE_VERTEX_COLORS 1\n#define MAX_SHADOWS 1024\n\n/*\n *<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">---<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">David Kastner</b><o:p class=""></o:p></div></div><div class=""><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><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(95, 95, 95);" class="">MIT | Kulik Lab</span><o:p class=""></o:p></div></div></div></div><div class=""><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: blue; text-decoration: underline;" class="">kastner.io</a></span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Tom Goddard <<a href="mailto:goddard@sonic.net" style="color: blue; text-decoration: underline;" class="">goddard@sonic.net</a>><br class=""><b class="">Date:<span class="apple-converted-space"> </span></b>Monday, September 27, 2021 at 4:30 PM<br class=""><b class="">To:<span class="apple-converted-space"> </span></b>David William Kastner <<a href="mailto:kastner@mit.edu" style="color: blue; text-decoration: underline;" class="">kastner@mit.edu</a>><br class=""><b class="">Cc:<span class="apple-converted-space"> </span></b>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="apple-converted-space"> </span></b>Re: [chimerax-users] Flat transparency setting absent</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Hi David,</span><o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt;" class="">ChimeraX does not have the flat transparency option. I have made a feature request for it</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt;" class=""><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5294" style="color: blue; text-decoration: underline;" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5294</a></span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt;" 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.</span><o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" 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.</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""> If you want to edit your ChimeraX distribution you can make it use flat transparency. The file to edit is (on Mac)</span><o:p class=""></o:p></div></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">ChimeraX-1.2.5.app/Contents/lib/python3.8/site-packages/chimerax/graphics/fragmentShader.txt</span><o:p class=""></o:p></div></div></blockquote><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">and you should add a "#" character in front of the following line using a text editor</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">so it becomes</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""># a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">This is the line in the graphics shader program that applies the angle dependent transparency. With this change, all transparency will be flat.</span><o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt;" class="">Tom</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><br class=""><o:p class=""></o:p></div></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Sep 27, 2021, at 12:43 PM, David William Kastner via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">ChimeraX community,<o:p class=""></o:p></div></div></div><div class=""><div class=""><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></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><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: blue; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0</span></a><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">David<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">---<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">David Kastner</b><o:p class=""></o:p></div></div></div><div class=""><div class=""><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><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(95, 95, 95);" class="">MIT | Kulik Lab</span><o:p class=""></o:p></div></div></div></div><div class=""><div class=""><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: blue; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">kastner.io</span></a></span><o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""></span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica; color: rgb(5, 99, 193);" class="">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size: 9pt; font-family: Helvetica;" class=""><br class="">Manage subscription:<br class=""></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica; color: rgb(5, 99, 193);" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p class=""></o:p></div></div></div></blockquote></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><br class=""><o:p class=""></o:p></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""></span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size: 9pt; font-family: Helvetica;" class=""><br class="">Manage subscription:<br class=""></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></div></div></blockquote></div></div></div></div></blockquote></div><br class=""></div></body></html>