<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"David Transparent";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Cambria","serif";
color:#17365D;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Cambria","serif";
font-variant:normal !important;
color:#17365D;
text-transform:none;
text-shadow:none;
font-weight:normal;
font-style:normal;
vertical-align:baseline;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body bgcolor=white lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Dear Tom,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Thanks for your great help. I made my image without ray tracing,
it is indeed nice too. But not as nice as ray-tracing…. </span><span
style='font-size:12.0pt;font-family:Wingdings;color:#17365D'>J</span><span
style='font-size:12.0pt;font-family:"Cambria","serif";color:#17365D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Thanks,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Maya<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'> Tom Goddard
[mailto:goddard@cgl.ucsf.edu] <br>
<b>Sent:</b> Wednesday, October 07, 2009 7:44 PM<br>
<b>To:</b> maya shcushan<br>
<b>Cc:</b> 'Chimera BB'<br>
<b>Subject:</b> Re: Chimera pov-tracing question<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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
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
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>
<br>
<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Dear Dr Goddard,</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'> </span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>You previously assisted me with other problems with Chimera, so
now I am asking your help again.</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>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</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'> </span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Thanks,</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Best,</span><o:p></o:p></p>
<p class=MsoNormal><b><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Maya Schushan</span></b><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>Department of Biochemistry</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Cambria","serif";
color:#17365D'>George S. Wise Faculty of Life Sciences<br>
Tel Aviv University</span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
</div>
</body>
</html>