OASIS and molecular-replacement model completion.

A method of dual-space molecular-replacement model completion has been proposed which involves the programs ARP/wARP, REFMAC, OASIS and DM. OASIS is used in reciprocal space for phase refinement based on models built by ARP/wARP. For this purpose, the direct-method probability formula of breaking SAD/SIR phase ambiguities has been redefined. During the phase refinement, phi(h)('') in the expression phi(h) = phi(h)('') +/- |Delta phi(h)| is redefined as a reference phase calculated from a randomly selected 5% of the atoms in the current structure model, while |Delta phi(h)| is defined as the absolute difference between the phase of the current model and phi(h)(''). The probability formula P(+)(Delta phi(h)) = (1/2) + (1/2) tanh {sin |Delta phi(h)| x [Sigma (h('))m(h('))m(h - h('))kappa(h,h(')) sin(Phi'(3) + Delta phi(h'best) + Delta phi(h - h'best)) + chi sin delta(h)]} is then used to derive the sign of Delta phi(h). In this way the '0-2pi' phase problem is reduced to a 'plus or minus' sign problem. The redefinition implies that during the refinement phases close to the true values will probably be kept unchanged, while those distant from the true values will probably undergo a large shift. This is the desired property of phase refinement. The procedure has been tested using protein diffraction data without SAD/SIR signals. The results show that dual-space MR-model completion making use of OASIS is much more efficient than that without.

SAD phasing by OASIS-2004: case studies of dual-space fragment extension.

The principle of dual-space phasing is used in dealing with protein SAD data. Four programs are involved in iterative dual-space fragment extension to improve automatic model building. OASIS-2004 is used to break the phase ambiguity intrinsic in the SAD experiment. In the initial cycle, discrimination of SAD phase doublets is performed by the direct method incorporating the known anomalous-scattering substructure. In subsequent cycles, discrimination is performed by the direct method incorporating both the known anomalous-scattering substructure and the partial protein structure obtained from model building in the preceding cycle. DM is used to improve direct-method phases via density modification. RESOLVE is used for initial model building and ARP/wARP is used to complete the structure. Case studies with three sets of difficult SAD data showed that the procedure is beneficial to high-throughput protein-structure determination and all of the four programs involved make their unique contribution to the process.