James,
What you want is something like SCWRL from the Dunbrack Lab. Minimization will
not get a sc out of an incorrect rotomer, and will not repack the protein in
the case of multiple mutations, SCWRL will. It can be downloaded for academic
use from here:
http://dunbrack.fccc.edu/SCWRL3.php/
Greg,
You can also use the alter command to change the vdw to the value you want.
This is often done with SAXS bead models so that they can then be surfaced.
alter (n. ca), vdw= 3
If this is set after the show spheres command the rebuild the view
rebuild
Hope this helps.
Best regards,
Mark
