Amino acid structure regularization (REFINE)

• Introduction.
• When to use CRUDE or REFI?
• Convergence.
• Fine refinement related options
  • Fine refinement (REFI)
  • Fine refinement (REFCNT)
  • Fixing atoms in refinement
    • Fixing atoms in refinement (FIXRNG)
    • Undoing fixing of atoms in refinement (NOFIX)
    • Fixing of alpha carbons in refinement (FIXCA)
    • Fixing of heavy atoms in refinement (FIXHAT)
    • Anchoring chain ends in refinement (ANCHOR)
    • Undoing anchoring of chain ends (NOANCH)
• Crude refinement related options
  • Crude refinement (CRUDE)
  • Closing Cys-Cys bridges (REFCYS)
• Options involving protons
  • Adding hydrogens (ADDHYD)
  • Deleting hydrogens (DELHYD)
  • Optimising proton positions (OPTHYD)
• Setting refinement parameters (PARAMS)
  • Number of cycles (NCYCS)
  • Number of iterations (NITS)
  • Desired Z-score (ZSCO)
  • Force for FIX options in REFI (FIXREF)
  • Level of detail (REFLEV)
  • Fix bad atoms flag (USEBAD)
  • Print warning level (WRNLEV)
  • directly poking REFI parameters with SETWIF
• Other options
  • Fixing residues on top of other residues (SNAPIT)