Refinement Checklist

• Convert starting model to TNT's ATOMC format.
  • When converting a PDB format file use from_pdb.
  • Generate a sequence file as well.
  • Edit the TNT control file (.tnt).
• Convert observed structure factors to TNT's HKL format.
  • Create separate test and working set .hkl files, if desired.
  • Run file(s) through correct for proper sort and asymmetric unit.
• Verify the coordinate and sequence files.
  • Check list produced by geometry.
    • Look for bonds between atoms which should not be bonded.
    • Look for bad contacts between atoms which should be bonded.
  • Recheck the geometry list as additional errors may appear.
• Verify the coordinate and HKL files.
  • Verify atom type of metal atoms.
  • Check the output of rfactor.
    • Look for low completeness of data set.
    • Look for unreasonable scale factors.
    • Look for unexpectedly high R value.
• If B scale factor > 3 use $tntbin/add_b to adjust individual B's.
• If MR or MS model run rigid body refinement (use COMBINE statements).
  • First refine one group for each chain, then one for each domain.
• Run 30 cycles of refinement (tnt 1 30)
  • If a particular class of geometry is too loose increase its weight.
  • If a particular class of geometry is too tight decrease its weight.
  • If a weight is changed run the refinement from the beginning.
• If the parameters of the model are still changing in the last cycle (use diffplot) run 10 more cycles.
• When the parameters have stopped changing calculate maps and examine the model on a graphics system (use make_maps and pekpik).

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