In my case although most of the hydrogen bonds imposed by secondary_structure.sheet() have been satisfied, the 3 strands do not adapt a beta sheet conformation. I tried to optimize only the 3 antiparallel beta strands by adapting the examples/automodel/model-segment.py script. After setting physical.values(default=1.0, h_bond=10.0)I get these violations in my log file:
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 8 H-bonding potential : 20 0 5 0.103 0.103 31.778 10.000
What type of restraints does secondary_structure.strand() impose to scale them up? The manual says phi and psi binormal restraints only, but in my log file I get this:
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
I also need some help interpreting the restraint files:
1. What do the different columns (apparently not the first 2) represent in the target.V99990001 file?
2. For what pattern should I search in the target.rsr file with respect to the beta sheet? Surprisingly I cant find any column having a Group value 8 (the 4th column) which corresponds to the H-bonding potential imposed by secondary_structure.sheet().