gelly Documentation : The BUSTER geometry function

The geometry function used in BUSTER refinements: TNT and improvements

• The original BUSTER-TNT refinement package combined the geometry function from the TNT refinement package with the maximum-likelihood X-ray objective function from BUSTER.
• The TNT geometry function is still used, but as BUSTER is now used to refine low-resolution structures it has been necessary to supplement the geometry function. These extensions have been implemented in the gelly program.
• If desired it is still possible to use the original TNT geometry function by specifying the '-M Geom2008' macro. The TNT function is potentially superior to the "improved" geometry for high resolutions.
• The improved geometry function (from July 2009 release) has:
  • Bond and Angle geometry restraints taken from the "EH99" set: R. A. Engh and R. Huber (2006) International Tables for Crystallography. Vol. F, Chapter 18.3, pp. 382-392. In particular, cis and trans proline use different sets of restraints. Most other refinement programs currently use the older EH (1991) target parameter sets.
  • An active torsion angle restraint for protein side chain chi angles. A sinusoidal functional form is used by default, to avoid discontinuities in gradients. See Appendix D
  • A restraint which can force chiral centres defined with the 'CHIRAL' card to adopt a given chirality. The functional form is a semiharmonic restraint on the improper torsions. It is only active for distorted chiral centres. It is described in Appendix E
  • Ideal-distance contact restraints replace the TNT "bad contacts". Both these terms are semi-harmonic penalty functions that become active when two atoms that are not bonded come into contact. Although the functional form is the same the TNT bad contact provides a stiff barrier when two atoms get very close (see TNT manual: CONTACT), whilst the ideal-distance contact term, as used in PROLSQ, becomes gently active when two atoms get closer than their ideal distance. For most atom pairs this occurs at the sum of the van der Waals radii. In the case of atoms that can hydrogen bond the ideal distance is reduced from the sum of the van der Waals radii.
  • Ideal-distance contacts are used for 1-4 contacts - that is, atoms that are at the ends of a torsion angle. 1-4 contacts can help prevent eclipsed torsions. and have particular importance in helping to ensure reasonable Ramachandran statistics. Ramachandran used consideration of 1-4 contacts for amino acid models in his original description of the diagram. The TNT geometry function does not consider 1-4 contacts.
  • The ideal-distance contact target parameters used are taken from those used in the refmac package
• The improved geometry is now used by default.
• The use of the improved geometry generally results in slightly lowered Rfree, improved Rfree-Rwork gaps and much improved Molprobity scores (see wiki).
• The improved geometry function has also enabled improvements to be made in the treatment of atoms at special positions. See Appendix F