The program SAPI and its applications. III. Determination of structures having pseudo-translational symmetry

Abstract

Optimization has been made of the program SAIl for automatic solution of structures having pseudotranslational symmetry. This includes: (1) floating default cutoff of E's; (2) automatic and user-adjustable balance between the number of systematically strong reflections and that of the systematically weak ones; (3) R factors for reflection subsets corresponding to the 'strong' group and the 'weak' groups. Examples on solving structures with pseudo-translational symmetry are discussed in detail. They include known as well as unknown structures and centrosymmetric as well as non-centrosymmetric structures, all of which can be solved starting from a default run of SAPI. IntroductionPseudo-translational symmetry often occurs in minerals and some important inorganic as well as organic crystals. Structures having pseudo-translational symmetry give rise to complicated positional ambiguity in real space or phase ambiguity in reciprocal space. Hence structure analysis of such kinds of crystals remains a difficult problem. The first example of applying direct methods to remove the phase ambiguity arising from pseudo-translational symmetry was given by Fan Hai-fu (1975). Since then the method has been greatly improved (Fan Hai-fu, He Luo, Qian Jin-zi & Liu Shi-xiang, 1978;Fan Hai-fu, Yao Jia-xing, Main & Woolfson, 1983) and finally incorporated into the program SAP! (Fan Hai-fu, 1986). For automatic discrimination of pseudo-translational symmetry and automatic grouping of the reflections accordingly, an additional subroutine AUTOGP is provided in SAPI (Fan Hai-fu, Yao Jia-xing & Qian Jin-zi, 1988). This enables structures having pseudo-translational symmetry, such as superstructures, to be solved in a fully automatic way. Apart from the above, optimization has also been made in SAPI to strengthen the power of dealing * Also in Department of Chemistry, Zhongshan University, Guangzhou, China.with structures having pseudo-translational symmetry. In this paper some treatments for the optimization are discussed and examples of practical applications are given. Default cutoff of E'sIn most direct-methods programs the default minimum value of normalized structure factors, E's, accepted for phase derivation is set to about 1.2. However, for structures having pseudo-translational symmetry, especially for superstructures, the total number of reflections will sometimes be much smaller than usual. In this case the number of E's accepted for phase derivation may not be enough to ensure a reliable result. In order to overcome this difficulty, the default minimum value of E's in SAIl is made automatically adjustable. The value 1.2 is used first; however it will be automatically changed by the program to 0.9 whenever the total number of input reflections is smaller than 500. Balance between 'strong' and 'weak' reflectionsOne special feature of structures having pseudo-translational symmetry is that the reflections can be classified into two categories, one systematically strong and the other systematically weak. In our method, thes...

FL-Online: An x-ray crystallographic web-server for atomic-scale structure analysis of biomolecule

“…As for SAPIonline and OASIS-online, there have been no changes to the previously published version, and the test results are consistent with the data we have presented. [24][25][26]28,29] For C-IPCASonline, we conducted a total of 60 blind tests, including 40 MR test cases and 20 SAD test cases. The MR search models were predicted by Alpha Fold2 and pre-processing by phaser.…”

“…[20,21] The first paper [20] extended the Sayre equation [22] by considering the existence of heavy atoms with known positions. A subsequent systematic study on pseudo-symmetries and phase ambiguities [23] led to the development of the program SAPI (structure analysis programs with intelligent control), [24][25][26] which is the first direct-method computer program capable of detecting and solving superstructures. SAPI was adopted by the Rigaku Corporation (Japan) and the Molecular Structure Corporation (United States) from 1986 until the early 1990s, serving as the main structure-solving program for small crystal structures.…”

STEP– a trial-and-error procedure for crystal structure determination. I. A description of the program systemSYSTEM90

“…It was originally solved by the program system SAPI (Fan, Yao & Qian, 1990), which has special provision for dealing with this kind of problem. In a default-mode run of SYSTEM90, set 23 gave a satisfactory value of XDFOM and the resultant E map showed all the non-H atoms.…”