Section 25.2.5.1.1. Model update

The quickest way to change the position of an atom substantially is not to move it, but rather involves a two-step procedure to remove it from its current (probably wrong) site and to add a new atom at a new (hopefully right) position. Such updating of the model does not imply that all rejected atoms are immediately repositioned in a new site, so the number of atoms to be added does not have to be equal to the number rejected.

Atom rejection in ARP is primarily based on the interpolated or electron density at its atomic centre and the agreement of the atomic density distribution with a target shape. Applied together, these criteria offer powerful means of identifying incorrectly placed atoms, but can suggest false positives. However, a correctly located atom that happens to be rejected should be selected again and put back in the model. Developments of further, perhaps more elegant, criteria may be expected in the future development of the technique.

Atom addition uses the difference or Fourier synthesis. The selection is based on grid points rather than peaks, as the latter are often poorly defined and may overlap with neighbouring peaks or existing atoms, especially if the resolution and phases are poor. The map grid point with the highest electron density satisfying the defined distance constraints is selected as a new atom, grid points within a defined radius around this atom are rejected and the next highest grid point is selected. This is iterated until the desired number of new atoms is found and reciprocal-space minimization is used to optimize the new atomic parameters.

Real-space refinement based on density shape analysis around an atom can be used for the definition of the optimum atomic position. Atoms are moved to the centre of the peak using a target function that differs from that employed in reciprocal-space minimization. The function used is the sphericity of the site, which keeps an atom in the centre of the density cloud but has little influence on the R factor and phase quality. It is only applicable for well separated atoms and is mainly used for solvent atoms at high resolution.

Geometrical constraints are based on a priori chemical knowledge of the distances between covalently linked carbon, nitrogen and oxygen atoms (1.2 to 1.6 Å) and hydrogen-bonded atoms (2.2 to 3.3 Å). Such constraints are applied in rejection and addition of atoms.