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Although PDB 2i9f is a virus nucleocapsid protein the crystal did not
contain whole or partial capsids so the capsid organization was not
determined from the crystallography. How do I know that? I displayed
the unit cell using the "Make Copies" button in the Unit Cell dialog
(menu Tools / Higher-Order Structure). There are 8 copies in the unit
cell in a clearly non-capsid arrangement.<br>
<br>
I do not know if there is other experimental data which determines the
capsid arrangement for this virus. Would need to look at the
associated journal article.<br>
<br>
Tom<br>
<br>
<br>
<blockquote cite="mid:50EA8E2F-28C9-4A8A-839B-8BE549E93DB3@cgl.ucsf.edu"
type="cite">
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<div>On May 25, 2010, at 10:39 PM, 江一波 wrote:</div>
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<div>hello meng!</div>
<div>how can i construct a virus by chimera?</div>
<div>i have get a <u><font color="#0000ff">nucleocapsid protein </font></u>
about a virus from <br>
<a moz-do-not-send="true"
href="http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current"
target="_blank">http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current</a></div>
<div>
<div>such as ,i get ID :<a moz-do-not-send="true"
class="qrb_structid"
href="http://www.rcsb.org/pdb/explore/explore.do?structureId=2I9F"
target="_blank" hasbox="2">2I9F</a> structure...one of a nucleocapsid
for a virus ...this is symmetrical structure!</div>
</div>
<div>i want construct a virus ...how can i do? is there
somethings paper about how to construct ?</div>
<div>thank you!!!</div>
</blockquote>
</div>
<br>
<div>Sometimes the PDB file will include matrix information needed to
build the capsid. If it does, you can use the Chimera tool "Multiscale
Models" to show the whole thing. However, the authors of this
structure (2I9F) did not include the necessary information in the PDB
file.</div>
<div><br>
</div>
<div>Next I tried to see if that structure is in VIPERdb, which would
also allow showing the whole thing in Chimera. However, when I tried
"File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was
not found.</div>
<div><br>
</div>
<div>Sorry, I don't have any ideas about how to make a whole capsid
from this structure.</div>
<div><br>
</div>
<div>A different structure that does include the information is 1POV.
If you open that one, then start Multiscale Models (under Tools...
Higher-Order Structure) and click the "Make models" button near the
bottom, it will show the whole capsid.</div>
<div><br>
</div>
<div>Please send Chimera questions to the <a moz-do-not-send="true"
href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
address. Thanks,</div>
<div>Elaine</div>
<div>------------------------------</div>
<div>
<div>Elaine C. Meng, Ph.D. </div>
<div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div>
<div>Department of Pharmaceutical Chemistry</div>
<div>University of California, San Francisco</div>
<div><br>
</div>
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