[Chimera-users] Elongating TMV capsid
goddard at sonic.net
Mon Aug 13 13:35:58 PDT 2012
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.
sym #0 group h,1.41,22.04,300 surf true
To get atomic models of all the subunits instead of surfaces just drop
the "surf true" option. But you may run out of memory.
> 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
> Dr. Jeremiah J. Gassensmith
> Stoddart Mechanostereochemistry Group
> Northwestern University
> 2145 Sheridan Road
> Evanston, IL 60208-3113
> Phone (W) +1(847)467-5936
> Fax +1(847)491-1009
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