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- 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
Dale Edwin Tronrud
Mon Jul 10 13:48:41 PDT 2000