Re: [modeller_usage] problem of strand/sheet

[Thomas Evangelidis <>]

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().