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<div class="moz-cite-prefix">Hi Jeremiah,<br>
<br>
The Chimera Multiscale Models dialog is just using the BIOMT
(biological unit matrix) records in the PDB file and for a long
helical virus or filament they usually only include less than 50
subunits. To make something longer use the Chimera "sym"
command. For example, I see in tobacco mosaic virus PDB structure
3j06 in the REMARK 350 BIOMT section it says the rise per subunit
is 1.41 Angstroms and rotation per subunit is 22.04 degrees. So
to make 300 subunits I use the sym command with those helical
parameters as follows.<br>
<br>
open 3j06<br>
sym #0 group h,1.41,22.04,300 surf true<br>
<br>
To get atomic models of all the subunits instead of surfaces just
drop the "surf true" option. But you may run out of memory.<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html</a><br>
<br>
Tom<br>
<br>
<br>
<br>
</div>
<blockquote
cite="mid:7CF42B29-4696-4D17-A20A-34BA7C788254@northwestern.edu"
type="cite">Hello,
<div><br>
</div>
<div>I've downloaded the tobacco mosaic virus structure from the
PDB and used Multiscale Models to build the biological unit.
Unfortunately, only about 45 or so of the 2200 protein monomers
show up. Is there a way I can multiply the biological unit to
elongate the TMV structure? I don't need all 2200 monomers, but
something a bit longer would be helpful.</div>
<div><br>
</div>
<div>Thanks!</div>
<div>Jeremiah<br>
<div>
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<br>
Dr. Jeremiah J. Gassensmith<br>
Stoddart Mechanostereochemistry Group<br>
Northwestern University<br>
2145 Sheridan Road<br>
Evanston, IL 60208-3113<br>
Phone (W) +1(847)467-5936<br>
Fax +1(847)491-1009<br>
</span>
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<br>
</div>
<br>
</blockquote>
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