Cd Zheng

OASIS: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data

The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located. OASIS adopts the CCP4 format [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763]. It applies a direct-method procedure to break the phase ambiguity intrinsic to one-wavelength anomalous scattering (OAS) or single isomorphous replacement (SIR) data.

Direct-method SAD phasing with partial-structure iteration: towards automation.

The probability formula of direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains partial-structure information in the form of a Sim-weighting term. Previously, only the substructure of anomalous scatterers has been included in this term. In the case that the subsequent density modification and model building yields only structure fragments, which do not straightforwardly lead to the complete solution, the partial structure can be fed back into the Sim-weighting term of the probability formula in order to strengthen its phasing power and to benefit the subsequent automatic model building. The procedure has been tested with experimental SAD data from two known proteins with copper and sulfur as the anomalous scatterers.

SAPI: a direct-methods program for finding heavy-atom sites with SAD or SIR data

SAPI is a CCP4-format program that applies a direct-methods procedure to find heavy-atom sites using single-wavelength anomalous dispersion (SAD) or single-isomorphous replacement (SIR) data. The program is designed to run in a fast (typical CPU time consumed is less than 1 min) and simple way. User input is kept to a minimum and the default parameter values are adequate in most cases. It can also be used to solve general small-molecule structures.

The Program SAPI and its Applications. II. The Combination of Patterson Superposition and Direct Methods

A minimum-function subroutine is included in the SAPI program. This enables the superposition of either two Patterson maps or a Patterson map with an E map. Both kinds of superposition can effectively combine Patterson and direct methods leading to results better than those from either of the two alone. Practical examples are given to elucidate the efficiency of such a combination.

Use of single isomorphous replacement data of proteins - resolving the phase ambiguity and a new procedure for phase extension.

A procedure combining direct methods and solvent flattening to break the phase ambiguity intrinsic to the single isomorphous replacement (SIR) technique has been tested with the experimental SIR data of the known protein RNase Sa at 2.5 A resolution. The use of direct methods provided better initial phases for the solvent-flattening procedure, while the solvent-flattening procedure greatly improved direct-method phases leading to a traceable Fourier map. A small subset of known phases at low resolution makes direct phasing of SIR data much easier. Accordingly a method for extending low-resolution phases to high-resolution ones is proposed making use of additional SIR information. This reduces the problem of finding a value in the range of 0-2pi for each unknown phase to that of just making a choice between two possible values. Tests with the known protein RNase Sa showed that the method is able to extend phases from a resolution of 6 to 2.5 A leading to an easily traceable Fourier map. The solvent-flattening technique and the combination of which with direct methods were used for the phase extension. Either procedure yielded reasonably good results, but on the whole, the result from the combination of direct methods with solvent flattening is better. Results of the latter procedure were further compared with that from direct phasing of the 2.5 A SIR data and with that from phase extension by solvent flattening without SIR information. An improvement gained by the use of SIR information is evident.

Applications of Direct Methods with Single Isomorphous Replacement or One-Wavelength Anomalous Scattering Data

Recent developments of our study have been concentrated on the following topics: 1) the accuracy of our Cochran-distribution-based probability formula: it has been shown that the results of the formula are much more accurate than what people would usually predict; 2) an iterative procedure of combining direct methods with the solvent flattening technique: test on the experimental single isomorphous replacement (SIR) data of the known protein RNase Sa showed considerable improvement to the previous procedure; 3) direct-method phasing of the one-wavelength anomalous scattering (OAS) data of an unknown protein: the result leads to a traceable Fourier map and thus to the solution of the structure.

Nuclear Physics Programs at HIRFL‐CSRm: A Status Report

An internal and an external target experiment, ETE and HPLUS, respectively, will be built at the HIRFL‐CSRm complex covering various nuclear physics programs. This talk introduces briefly the conceptual designs and the main physical interests of these two experiments. Parallel R&D works for the sub‐detectors of ETE and HPLUS have been started. The current status is documented.

Protein MIR phases improved by direct methods

Direct methods have been applied to multiple-isomorphous replacement (MIR) data of a known protein containing 682 amino-acid residuals in the asymmetric unit. The data set consists of 14,500 unique reflections at 3.0 Åresolution with F(obs) greater than 2σ. Test calculation showed that the phases from conventional MIR phasing could be considerably improved by direct methods. Main points of the new phasing procedure are as follows. (i) Conventional MIR phasing is first performed. Phases with a figure of merit greater than a certain limit, say 0.99, are accepted as the input to the following step. (ii) The MIR data are divided into n-sets (n equals the number of heavy-atom derivatives) of single isomorphous replacement (SIR) data. Each SIR set is treated by direct methods separately to break the phase ambiguity with starting phases from step (i). (iii) Direct-method phases from different sets of SIR data are combined to give a unique set of phases. (iv) Resultant phases from step (iii) are further combined with that of step (i) to give the final phases. The result in comparison with that from conventional MIR phasing is shown below. Averaged figure of merit: increased from 0.71 to 0.80. Correlation coefficient: increased from 0.51 to 0.55. Fobs weighted averaged phase error: decreased from 58.74° to 56.10°. This project was initiated according to a very helpful discussion with Professor Liang Dong-cai.