On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen
I set main.secondary_structure_restraints = True and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.
My DNA looks like this:
HETATM 1 O5* Ad D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5* Ad D 1 13002 6701 15042 3404 -258 -1747 O
Is there any reason it wouldn't be recognized by PROBE?
Jeff says that PROBE probably won't recognize "Ad" (it expects "dA" instead), and the default behavior probably requires O5', not O5*. The atom naming we can probably work around, the residue names are more difficult. What program generated these residues? If you can send us the model (or just enough of it to have base pairs, actually), we'll take a look. -Nat