title: Windex: a toolset for indexing helices.
abstract: We describe here a set of procedures and algorithms that may be used as an aid in determining the indexing rule of a helical specimen. Crystallizing macromolecules into helical arrays has the potential to speed up and simplify the process of three-dimensional reconstruction of the macromolecular structure. The process of helical reconstruction has been largely automated except for the critical first step of indexing the helical diffraction pattern. This is quite often the rate-limiting step in the overall process, particularly in the case of large helical tubes, which have complicated helical diffraction patterns that may vary from tube to tube. We have developed a set of procedures, supported by a graphical user interface, that provide a straightforward and semi-automated approach to indexing a helical structure. The new procedures have been tested using a number of helical specimens, including TMV, acto-myosin, decorated microtubules, and a variety of helical tubes of a bacterial membrane protein.
authors.affiliation: Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Ward
authors.forename: Michael F
authors.initials: MF
authors.lastname: Moody
authors.forename: Brian
authors.initials: B
authors.lastname: Sheehan
authors.forename: Ronald A
authors.initials: RA
authors.lastname: Milligan
authors.forename: Bridget
authors.initials: B
authors.lastname: Carragher
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000737:chemistry; D000205:Actomyosin / Q000737:chemistry; D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology; D005583:Fourier Analysis; D046911:Macromolecular Substances; D008870:Microtubules / Q000737:chemistry; D015233:Models, Statistical; D012984:Software; D014027:Tobacco Mosaic Virus / Q000737:chemistry
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D046911:Macromolecular Substances; C079726:MsbA protein, Bacteria; D000205:Actomyosin