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.

    http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html

  Tom