<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Hi John,<br>
<br>
Glass surfaces show reflections and also refraction (bending) of
light passing through the surface. Chimera does not do either of
those two effects. So Chimera surfaces never look like glass. But
here are the 3 most important Chimera settings for making a nice
looking transparent surface.<br>
<br>
1. Transparency. Make a map surface transparent using the color
button below the volume dialog histogram, click the "opacity"
button, and adjust the A value which is opacity. Or use the volume
command, for example, "volume #0 color .7,.8,.9,.7" specifying red,
green, blue and opacity values on a scale of 0 to 1.<br>
<br>
2. "Glossy" lighting. Use menu Tools / Viewing Controls / Lighting
and change Quality from "normal" to "glossy". This gives nicer
specular highlights (bright spots) on the surface calculating them
per-pixel instead of per surface triangle vertex. This option may
not be available with very old graphics cards.<br>
<br>
3. Silhouette edges and white background. Black edges on your
surface with a white background make the depth easier to perceive.
Enable that with commands "set silhouette" (or menu Tools / Viewing
Controls / Effects) and "set bg_color white" (or menu Actions /
Color / All Options).<br>
<br>
I've attached an example image made with these commands:<br>
<br>
open emdbID:1962<br>
volume #0 color .7,.7,.7,.5 level 1<br>
set bg_color white<br>
set silhouette<br>
open 4a0w<br>
rainbow chain<br>
~rib ~:.A,.M<br>
<br>
See the image tutorials in the Chimera manual for more ideas<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html</a><br>
<br>
Tom<br>
<br>
<blockquote
cite="mid:00ef01cd2d1b$e8b42760$ba1c7620$@imperial.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:PMingLiU;
panose-1:2 2 5 0 0 0 0 0 0 0;}
@font-face
{font-family:PMingLiU;
panose-1:2 2 5 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"\@PMingLiU";
panose-1:2 2 5 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";}
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-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></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]-->
<div class="WordSection1">
<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am trying to show a density map as a
glassy surface within which various molecular chains have been
fitted. Can anyone please tell me how to produce such a
glassy surface for the density map in Chimera?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">John Squire<o:p></o:p></p>
<div
style="mso-element:para-border-div;border:none;border-bottom:solid
windowtext 1.5pt;padding:0cm 0cm 1.0pt 0cm">
<p class="MsoNormal" style="border:none;padding:0cm"><o:p> </o:p><br>
</p>
</div>
</div>
</blockquote>
<br>
</body>
</html>