|The BUSTER geometry function
gelly Documentation : The BUSTER geometry function
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- 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
- 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
Page Author: Oliver S. Smart
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Last modification: 07.06.09