The parameters of the flat bulk-solvent model have been studied. A procedure for their search is suggested which allows improvement of the correspondence between the calculated and experimental data.
PDB2INS reads a Protein Data Bank (PDB)-format file and writes a .ins file containing the atom data and instructions for SHELXL refinement. Given only the PDB code of a deposited structure, it automatically creates both files (.ins and .hkl) necessary to refine the structure.
A method is described for the refinement of an electron-density model against a set of structure-factor observations which does not rely on atomic parameters. The effective level of detail in the parameterization can be varied to ensure that the refinement is well determined at any resolution supported by the data.
Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules.
Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.
A set of restraints for an iron–sulfur cluster based on small-molecule structures was generated and tested in structure refinement. Additionally, the small-molecule structures also provided bond and angle restraints for linking the cluster to the coordinating cysteine residues.