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Hi Maya,<br>
<br>
Your mesh is transparent in the povray image (zoom in on the image
and look at the mesh lines) but I guess is much less transparent than
in the Chimera window. I ran some test images with the current Chimera
1.4 daily build which also showed the povray mesh looked much different
(darker, thicker and less transparent) than in the Chimera window.
While we have improved the match between povray images and what you see
in the Chimera window it is still very bad. Dozens of messages on the
chimera-users mailing list relate to the poor quality of Chimera Povray
images. <br>
<br>
<a class="moz-txt-link-freetext" href="http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users+-filetype%3Agz+site%3Awww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users+-filetype%3Agz&aq=f&oq=&aqi=">http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users+-filetype%3Agz+site%3Awww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users+-filetype%3Agz&aq=f&oq=&aqi=</a><br>
<br>
As suggested in the following message, with these poor quality povray
results a better presentation can almost always be obtained by not
using povray:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html</a><br>
<br>
Attached are 5 test images showing some of the problems. 1mwm chain A,
molmap 6 angstroms.<br>
<br>
test.png - povray transparent mesh 0.24, appears very dark<br>
test2.png - povray transparent mesh 0.04, black specks all over the mesh<br>
test4.png - povray transparent surface 0.24, ugly multilayer mosaic<br>
test5.png - no povray, transparent surf 0.24, glossy lighting,
silhouette edges<br>
test6.png - no povray, same as test5 but mesh.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Chimera pov-tracing question<br>
From: maya shcushan<br>
To: 'Thomas Goddard'<br>
Date: 10/7/09 9:59 AM<br>
<blockquote cite="mid:009b01ca476f$82d59da0$8880d8e0$@com" type="cite">
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<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">Dear
Dr Goddard,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">You
previously assisted me with other problems with Chimera, so
now I am asking your help again.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">I
have a density map and a structure mapped on it. I showed the
map as transparent mesh, and tried to pov-ray the image. However, the
picture
came up with the map not transparent (attached). Do you have any idea
how to
resolve this issue, making the map transparent in the image as it is in
the
main window<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><b><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">Maya
Schushan<o:p></o:p></span></b></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">Department
of Biochemistry<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Cambria","serif"; color: rgb(23, 54, 93);">George
S. Wise Faculty of Life Sciences<br>
Tel Aviv University<o:p></o:p></span></p>
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</blockquote>
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