<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Jethro, Jaime,<div><br></div><div> We have worked around the Mac Yosemite graphics driver bug that causes dim molecule display of atoms and bonds in Chimera and will be making a new Chimera release in a week or two. Currently the fix is in the Chimera daily builds and the Chimera release candidate. The fix maintains high graphics rendering performance and does not disable DrawElementsInstanced.</div><div><br></div><div> Thanks for reporting the problem.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br><div><div>On Oct 8, 2014, at 2:27 PM, Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Disabling DrawElementsInstanced will slow down rendering of atoms shown as spheres and bonds shown as cylinders by about a factor of 10-30x, but you probably won’t notice unless you are looking at more than 20,000 atoms. Disabling Shading basically turns off all modern 3d graphics based on GPU shader programs — you’ll then be relying on very old Chimera fallback graphics code. So I suggest keeping shading on if possible.<div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br><div><br><div><div>On Oct 8, 2014, at 2:10 PM, Jethro Hemmann <<a href="mailto:j.hemmann@gmail.com">j.hemmann@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div>Thank you Conrad and Jaime for you answers.<br></div>The debug options indeed fixed the problem. Instead of disabling DrawElementsInstanced, disabling Shading also seems to work. <br><br></div>Jethro<br></div><div class="gmail_extra"><br><div class="gmail_quote">2014-10-08 23:04 GMT+02:00 Jaime Stark <span dir="ltr"><<a href="mailto:jlstark@wisc.edu" target="_blank">jlstark@wisc.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">I was seeing this problem too in Yosemite. It’s easily fixed by turning on the “Debug OpenGL on startup” as Conrad suggests. When you next start Chimera, in the OpenGL options that popup, disable DrawElementsInstanced. That will fix the dim coloring for small molecules on Yosemite for now.<div><br></div><div>Jaime<br><div>
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><br><font color="#919191">===================================<br>Jaime L. Stark, Ph.D.<br>Postdoctoral Research Associate at NMRFAM</font></div><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><font color="#919191">University of Wisconsin - Madison<br>Department of Biochemistry</font></div><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><span style="color:rgb(153,153,153);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">DeLuca Biochemical Laboratories</span><font color="#919191"><br>Room B160H</font></div><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><font color="#919191">433 Babcock Drive<br>Madison, WI 53706<br>Email: </font><a href="mailto:jlstark@wisc.edu" target="_blank">jlstark@wisc.edu</a><font color="#919191"><br>Phone: (608) 262-0459<br>Website: </font><a href="http://www.nmrfam.wisc.edu/" target="_blank">http://www.nmrfam.wisc.edu</a><font color="#919191"><br>===================================</font></div><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><font color="#919191"><br></font></div><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><font color="#919191"><br></font></div></div></div></div></div></div><br></div><br><br>
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<br><div><blockquote type="cite"><div>On Oct 8, 2014, at 3:48 PM, Conrad Huang <<a href="mailto:conrad@cgl.ucsf.edu" target="_blank">conrad@cgl.ucsf.edu</a>> wrote:</div><br><div>Unfortunately, we have not tested Chimera on Yosemite yet. It is highly likely that there is some OpenGL issue given the images that you are seeing. We will try to get to this soon, but we're pretty tight on programmer resources.<br><br>If you feel adventurous (which I assume you are since you're running Yosemite :-) ), you can try playing with some OpenGL options by going to the General category in Preferences and turn on "Debug OpenGL on startup". The next time you start Chimera, it should display a dialog where you can selectively turn certain OpenGL options on and off (see <a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html</a>). If you discover anything, please let us know.<br><br>Conrad<br><br>On 10/8/2014 2:31 AM, Jethro Hemmann wrote:<br><blockquote type="cite">Hi,<br><br>I'm currently using Chimera on my Macbook running the public beta of<br>Yosemite.<br><br>The colors of the molecules appear very dim and they are hard to<br>recognize, as can be seen in the attached screenshot. In this example,<br>the lipid chains are colored orange, while the water molecules should by<br>cyan.<br>The colors in the menu Actions --> Color seem to appear with their<br>correct brightness, although.<br><br>I also tried the daily build of the alpha version of Chimera, but the<br>problem persists.<br><br>Is this problem related to Yosemite? Or do I have to adjust some settings?<br><br>Thanks a lot,<br><br>Jethro<br><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br><br></blockquote>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div></div></div><br>_______________________________________________<br>
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