title: ACORN: a review.
abstract: The ACORN system was originally developed as a means of ab initio solution of protein structures when atomic resolution data were available. The first step is to obtain a starting set of phases, which must be at least slightly better than random. These may be calculated from a fragment of the structure, which can be anything from a single metal atom to a complete molecular-replacement model. A number of standard procedures are available in ACORN to orientate and position such a fragment. The fragment provides initial phases that give the first of a series of maps that are iteratively refined by a dynamic density-modification (DDM) process. Another FFT-based procedure is Sayre-equation refinement (SER), which modifies phases better to satisfy the Sayre equation. With good-quality atomic resolution data, the final outcome of applying DDM and SER is a map similar in appearance to that found from a refined structure, which is readily interpreted by automated procedures. Further development of ACORN now enables structures to be solved with less than atomic resolution data. A critical part of this development is the artificial extension of the data from the observed limit to 1 A resolution. These extended reflections are allocated unit normalized structure amplitudes and then treated in a similar way to observed reflections except that they are down-weighted in the calculation of maps. ACORN maps, especially at low resolution, tend to show C atoms less well, in particular C(alpha) atoms which fall within the first diffraction minimum of their three neighbours. Two new density-modification procedures (DDM1 and DDM2) and a density-enhancement procedure (ENH) have been devised to counter this problem. It is demonstrated that high-quality maps showing individual atoms can be produced with the new ACORN. ACORN has also been demonstrated to be very effective in refining phase sets derived from physical processes such as those using anomalous scattering or isomorphous derivative data. Future work will be directed towards applying ACORN to resolutions down to 2 A.
authors.affiliation: York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, England. yao@ysbl.york.ac.uk
authors.forename: J X
authors.initials: JX
authors.lastname: Yao
authors.forename: E J
authors.initials: EJ
authors.lastname: Dodson
authors.forename: K S
authors.initials: KS
authors.lastname: Wilson
authors.forename: M M
authors.initials: MM
authors.lastname: Woolfson
mesh_terms: D003198:Computer Simulation / Q000266:history; D018360:Crystallography, X-Ray / Q000266:history; D030562:Databases, Protein / Q000266:history; D049673:History, 20th Century; D049674:History, 21st Century; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software / Q000266:history
chemical_list: D011506:Proteins