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<DIV><FONT size=2 face=Arial>Hi Elaine and Tom</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Thank you for the suggestions, I haven't had a
chance to try any of them. But I hope to do this in the next couple of
days.</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Regards</FONT></DIV>
<DIV><FONT size=2 face=Arial>Brian</FONT></DIV></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="FONT: 10pt arial; BACKGROUND: #e4e4e4; font-color: black"><B>From:</B>
<A title=meng@cgl.ucsf.edu href="mailto:meng@cgl.ucsf.edu">Elaine Meng</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=blgrech@ozonline.com.au
href="mailto:blgrech@ozonline.com.au">Brian & Lanie Grech</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Cc:</B> <A title=chimera-users@cgl.ucsf.edu
href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Saturday, October 16, 2010 2:49
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [Chimera-users] Molecule
fusing</DIV>
<DIV><BR></DIV>Hi Brian,
<DIV>Figure 1A shows a density map that has been segmented and colored, with
an octant chopped out.</DIV>
<DIV><<A
href="http://www.pnas.org/content/106/26/10644.long">http://www.pnas.org/content/106/26/10644.long</A>></DIV>
<DIV><BR></DIV>
<DIV>Chimera does have tools for building multimers using symmetry
information, see Multiscale Models, Unit Cell, and command "sym."
However, these just generate and place the extra copies, either as
low-res surfaces (Multiscale Models) or as full atomic copies (Unit Cell).
There is no "fusing" or generating a density map from the whole
assembly. Each chain is separate.</DIV>
<DIV><<A
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html</A>></DIV>
<DIV><<A
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html</A>></DIV>
<DIV><<A
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</A>></DIV>
<DIV><BR></DIV>
<DIV>You could get a whole assembly at atomic detail and then simulate a
density map from it with the "molmap" command.</DIV>
<DIV><<A
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</A>></DIV>
<DIV>However, that would be very inefficient and might overload your system
and take forever. That is why Multiscale Models makes the copies as
low-resolution surfaces by default. You might want to take a look at
Multiscale Models and see if what it does meets your needs before trying that
more drastic approach. An easy way to try it is to use File... Fetch by
ID and get something from viperdb, which will automatically use Multiscale
Models to build the capsid. Besides the example given in the dialog, I
like 1pov (poliovirus) and 1bbt (foot and mouth disease virus).</DIV>
<DIV><BR></DIV>
<DIV>I hope this helps,</DIV>
<DIV>Elaine</DIV>
<DIV>
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class=Apple-style-span>
<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></SPAN></DIV>
<DIV>
<DIV>On Oct 14, 2010, at 7:50 PM, Brian & Lanie Grech wrote:</DIV><BR
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<DIV><FONT face=Arial>
<DIV style="MARGIN: 0cm 0cm 0pt"><FONT size=2>Hi Sir/Madam</FONT></DIV>
<DIV style="MARGIN: 0cm 0cm 0pt"><O:P><FONT size=2> </FONT></O:P><SPAN
style="FONT-SIZE: small" class=Apple-style-span>I want to create models
which consist of multiple protein molecules, in which the individual protein
molecules are fused together to form a single structure. Something like the
scanning 3D maps produced by electron microscopes. Is it possible to do this
with the Muliscale Models tool or some other tool or method in
Chimera?</SPAN></DIV>
<DIV style="MARGIN: 0cm 0cm 0pt"><O:P><FONT size=2></FONT></O:P></DIV>
<DIV style="MARGIN: 0cm 0cm 0pt"><FONT size=2>An example of what I want to
do appears in the cutaway rotavirus illustration (Fig. 1A) in Chen and
colleagues paper, titled, “Molecular interactions in rotavirus assembly and
uncoating seen by high-resolution cryo-EM” (PNAS, vol. 106. no. 26, p.
10644). In this illustration the yellow triangular shaped structure are
multiple VP7 molecules fused together.</FONT></DIV>
<DIV style="MARGIN: 0cm 0cm 0pt"><O:P><FONT size=2></FONT></O:P></DIV>
<DIV style="MARGIN: 0cm 0cm 0pt"><FONT size=2>Regards</FONT></DIV>
<DIV style="MARGIN: 0cm 0cm 0pt"><FONT size=2>Brian
Grech</FONT></DIV></FONT>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><FONT face=Arial><FONT
size=2></FONT></FONT></P></DIV></DIV></SPAN></BLOCKQUOTE></DIV><BR></DIV><BR><PRE>_____________________________________________________
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