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fffear 1.2. Kevin Cowtan’s Fast Fourier FEAture Recognition program searches for molecular fragments in poor quality electron density maps.
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fffear 1.2 Kevin Cowtan’s Fast Fourier FEAture Recognition program searches for molecular fragments in poor quality electron density maps. The main application is the detection of helices in poor maps, and of beta strands in intermediate quality maps. It is also possible to use electron density as a search model, allowing the location of NCS elements. Top left: The best region of a low quality 6Å SIR map. One helix shows a cylinder of density, others are broken. The map shows no indication of the register of the helix. Bottom left: The result of a fragment search in the 6Å SIR map. Four of the six helices have been found. The register of the helices is correct, and in many cases C-alpha atoms have been positioned correctly, although the chain direction is unreliable. Reference: Cowtan, K. (1998) Acta. Cryst.D54 750-756 “Modified phase translation functions and their application to molecular fragment location.” See also: http://www.ysbl.york.ac.uk/~cowtan/ CCP4 Version 4.1 ... The most recent version of the CCP4 suite is 4.1, which was released at the end of January 2001, with a minor patch release shortly after. Below are some of the highlights in this latest version of the Suite. Refmac5 & sketcher MOSFLM v6 REFMAC is Garib Murshudov’s macromolecular refinement program. MOSFLMis a versatile program for integrating area detector data, dealing with all commonly used area detectors in macromolecular crystallography. It is easy to use, offering both graphical and command-line interfaces, and its output feeds directly into CCP4 data reduction programs. This is a major new version of REFMAC which can now automatically prepare geometric restraints, and identify disulphides, covalent bonds and cis-peptides prior to refinement - dispensing with the old PROTIN program. New libraries for nucleotides, sugars and some common ligands are also provided. Interaction with the libraries is through Alex Vagin’s LIBCHECK program, and CCP4i includes the monomer SKETCHER as an interface (see left). REFMAC5 also offers an improved bulk solvent correction and the option of refining TLS parameters. Below:The crystal structure of GerE (a transcription activator from Bacillus subtilis) was solved by MAD phasing using the Se signal, which revealed six monomers arranged as three pairs of dimers (see figure). The rigid body motion of the monomers necessitated a TLS description during refinement with REFMAC5; using this parameterisation reduced the crystallographic and free R factors by 5% and 5.5% respectively for data to 2.05Å, and substantially improved the map quality. See also: http://www.mrc-lmb.cam.ac.uk/harry/mosflm Left: an application of the rigid body test to a 1.15Å structure of a myoglobin-CO complex (PBD id 1a6g). The plot shows the results of the test between all pairs of atoms, averaged over chosen bins. The lighter areas indicate pairs of atoms that satisfy the test most, and hence may form quasi-rigid groups. Atomic U’s include many contributions and there is therefore always a lot of noise, but in this case the putative rigid groups nicely pick out helices or groups of helices in the myoglobin which are thought to act as rigid groups. anisoanl Martyn Winn’s analysis program provides some simple tools for analysing anisotropic displacement parameters (atomic U’s), as obtained from atomic resolution refinements. A variety of plots are given, Rosenfield’s rigid-body postulate can be assessed, and TLS parameters can be fitted for possible rigid groups. Reference: V.M.A. Ducros, R.J. Lewis, C.S. Verma, E.J. Dodson, G. Leonard, J.P. Turkenburg, G.N. Murshudov, A.J. Wilkinson and J.A. Brannigan, J. Mol.Biol. (2001) 306 759-771 See also: Winn, M.D. (2001) “ANISOANL - analysing anisotropic displacement parameters”, CCP4 Newsletter 39 (March 2001) 13-22. Roadmaps & Tutorial2000 Roadmaps are intended to give an overview of the different stages of the structure determination process, and are easily accessible from the CCP4i documentation. The Tutorial2000 material offers a set of CCP4i-based tutorials in the areas of Data Processing, MAD Phasing, Molecular Replacement, and Refinement using REFMAC5. Roadmaps: http://www.ccp4.ac.uk/ccp4/ccp4i/help/roadmaps/ Tutorial2000: http://www.ccp4.ac.uk/ccp4/examples/tutorial2000/html/ CCP4i-graphical user interface Other programs • CCP4i is the CCP4 graphical user interface. • This latest version includes a number of improvements as well as new interfaces for: • BAVERAGE • CONTACT • FFFEAR • DMMULTI • DTREK2MTZ • SIGMAA • WATERTIDY • CAVENV - produces maps to facilitate the visualisation of cavities • COMBAT - create multirecord MTZ files for input to SCALA • DM 2.1 - density modification package. • DTREK2MTZ - convert d*trek scalemerge output to MTZ format • MAP2FS - jiffy to convert CCP4 maps to XtalView fsfour format • MOLREP 6.2.5- automated molecular replacement program • ROTGEN - simulate rotation diffraction images for collection strategy • RSPS 4.2 - real space patterson search program • SCALA 2.7.5 - scale together multiple observations of reflections. MapSlicer Peter Briggs’ utility program for viewing contoured sections in CCP4 maps - see CCP4 newsletter 39 (March 2001) 45-48. For more on CCP4i see: http://www.ccp4.ac.uk/ccp4i_main.html Future developments … New Libraries, Automation, Molecular Graphics
