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Hi Yen-Chywan,<br>
<br>
To show a simple icosahedral cage with 12 triangles use the
"shape" command.<br>
<br>
shape icos radius 170 orient 222r mesh true divisions 1 color
blue linewidth 4<br>
<br>
Here's documentation<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/shape.html#icosahedron">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/shape.html#icosahedron</a><br>
<br>
Tom<br>
<br>
<blockquote type="cite">
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Dear
Tom,</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">If you
look at the attach figure carefully, you will find it is not
hkcage. In the figure it connect all the 5 fold vertex. How
can we generate it?</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
<span style="color: rgb(31, 73, 125);">Yen-Chywan</span></blockquote>
<br>
<br>
<blockquote cite="mid:4DCB4191.9030100@sonic.net" type="cite">
<meta content="text/html; charset=ISO-8859-1"
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Hi Yen-Chywan,<br>
<br>
The Chimera "hkcage" command makes a cage of pentagons and
hexagons to show virus symmetry. For example,<br>
<br>
open emdbID:1058<br>
hkcage 1 1 radius 170 orient 222r linewidth 4 color blue<br>
<br>
The hkcage command has options for the lattice parameters for your
virus, its radius, what icosahedral coordinate system is being
used. Here's the documentation.<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html</a><br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage">http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage</a><br>
<br>
The meshmol command can make the edges of the cage cylinders
instead of lines.<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html</a><br>
<br>
The HHMI virus viewer Chimera tool is not part of the standard
Chimera distribution. It was made for a CD distributed by the
Howard Hughes Medical Institute<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://wwwtest.cgl.ucsf.edu/Outreach/ViralOutbreak/index.html">http://wwwtest.cgl.ucsf.edu/Outreach/ViralOutbreak/index.html</a><br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.hhmi.org/catalog/main?action=product&itemId=366">http://www.hhmi.org/catalog/main?action=product&itemId=366</a><br>
<br>
We don't distribute it separately.<br>
<br>
Tom<br>
<br>
<blockquote
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<p class="MsoNormal">Dear Tom,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I attend Scripps cryoEM workshop before
and meet you there.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Attach please find a screen capture of a
virus. But there is a icosahedra cage. My question is how to
display that cage with my virus volume?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I did find it in HHMI virus viewer demo
movie. But where can download this viewer?<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">Yen-Chywan<o:p></o:p></p>
</div>
</blockquote>
<br>
<br>
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<br>
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