Structure verification (CHECK)

• Introduction.
• X-ray or NMR?
• Completely checking a protein (FULCHK)
• Running only a subset of the checks (FSTCHK)
• Starting a new summary file (NEWCHK)
• Individual Checks: Atoms and coordinates
  • Checking chain names (CHNCHK)
  • Checking coordinate rounding (CRDCHK)
  • Nomenclature checks (NAMCHK)
  • Atomic occupancy check (WGTCHK)
  • B-factor check (XBFCHK)
• Individual Checks: Symmetry related
  • Checking distance of atoms to symmetry axes (AXACHK)
  • Checking validity of water molecules (H2OCHK)
  • Matthews' coefficient (MVMCHK)
  • Non-crystallographic symmetry checks (NCSCHK)
  • Verifying symmetry information (SYMCHK)
• Individual Checks: Geometry related
  • Bond angle check (ANGCHK)
  • Checking bondlengths (BNDCHK)
  • Checking torsion angles (CHICHK)
  • Omega check (OMECHK)
  • Side Chain planarity check (PLNCHK)
  • Side Chain planarity check 2 (PL2CHK)
  • Side Chain planarity check 3 (PL3CHK)
  • Proline puckering check (PUCCHK)
  • Ramachandran analysis (RAMCHK)
  • Checking the hand of chiral atoms (HNDCHK)
• Individual Checks: DG Database related
  • Backbone conformation check (BBCCHK)
  • Chi-1/Chi-2 correlation check (C12CHK)
  • Checking for peptide plane flips (FLPCHK)
  • Looking for rotamer normality (ROTCHK)
• Individual Checks: Packing and Folding
  • Checking for unusual short distances (BMPCHK)
  • Checking first generation packing quality (QUACHK)
  • Checking second generation packing quality (NQACHK)
  • Input Output distribution check (INOCHK)
• Individual Checks: Other tools
  • Verifying normality of surfaces (ACCCHK)
  • Unsatisfied buried H-bond donors and acceptors (BPOCHK)
  • Hydrogen bond network checks (HNQCHK)