[Chimera-users] Elongating TMV capsid

Tom Goddard goddard at sonic.net
Mon Aug 13 13:35:58 PDT 2012

Hi Jeremiah,

   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.

open 3j06
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.



> Hello,
> 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.
> Thanks!
> Jeremiah
> 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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