Properties used to control details of structural refinement against experimental data sets and advanced force fields.
X-ray, Neutron and Real Space Refinement Properties
| Property | Type | Default | Description |
|---|---|---|---|
| fostring | string | null | title of the Fo column in the input MTZ file (if it is not one of the default values of F, Fo, Fp or Fobs) |
| sigfostring | string | null | title of the sigFo column in the input MTZ file (if it is not one of the default values of sigF, sigFo, sigFp or SigFobs) |
| rfreestring | string | null | title of the Rfree column in the input MTZ file (if it is not one of the default values of Rfree, freeR, freeRflag, Rfreeflag, test, freer_flag or R-free-flags) |
| use_3g | boolean | true | uses 3 Gaussians in form factor equation rather than 6 (set to false for atomic resolution data) |
| aradbuff | double | 0.5 | atom radius buffer for sampling grid density, added to dynamically determined radius |
| splinefit | boolean | true | apply a resolution dependent spline fit between Fo and Fc |
| fsigfcutoff | double | -1.0 | F/sigF cutoff (negative: all values read in) |
| resolution | double | -1.0 | resolution cutoff (negative: all data read in) |
| rfreeflag | integer | -1 | integer flag for Rfree reflections (negative: automatically determined from data) |
| nbins | integer | 10 | number of bins to divide data into for purposes of statistics/sigmaA fits |
| gridsearch | boolean | false | grid over bulk solvent parameters to determine optimal starting values |
| xrayscaletol | double | 1e-4 | gradient rms tolerance for scaling |
| sigmaatol | double | 1.0 | gradient rms tolerance for sigmaA fit |
| xweight | double | 1.0 | weight for summed diffraction data (weights for individual data sets are provided at the script level) |
| bsimweight | double | 1.0 | harmonic restraint B-factor weight between bonded atoms (increase to 5 or 10 for low resolution structures if necessary) |
| bnonzeroweight | double | 1.0 | entropy term to prevent nonzero B factors |
| bmass | double | 5.0 | fictitious mass to assign to B factors for extended Lagrangian methods |
| residuebfactor | boolean | false | set to true to refine a B factor for each residue |
| nresiduebfactor | integer | 1 | number of residues per B factor (requires residuebfactor to be true) |
| addanisou | boolean | false | set to true to add ANISOU records to the PDB file based on isotropic B factors |
| refinemolocc | boolean | false | set to true to refine occupancies of HETATMs, only performed if hetatms are in alternate conformers or occ < 1.0 |
| occmass | double | 10.0 | fictitious mass to assign to occupancies for extended Lagrangian methods |