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Ccp4 Newsletter on Protein Crystallography

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Ccp4 Newsletter on Protein Crystallography CCP4 NEWSLETTER ON PROTEIN CRYSTALLOGRAPHY An informal Newsletter associated with the BBSRC Collaborative Computational Project No. 4 on Protein Crystallography. Number 39 March 2001 Contents 1. News from CCP4 Peter Briggs, Martyn Winn, Sue Bailey, Alun Ashton, David Brown, Charles Ballard 2. SC: measuring shape complementarity at protein-protein interfaces Mike Lawrence 3. ANISOANL - analysing anisotropic displacement parameters Martyn Winn 4. LAPACK in CCP4 4.1 Peter Briggs 5. A System for storing Annotated Diffraction Data John Badger 6. CCP4 Molecular Graphics Liz Potterton 7. ARP/wARP goes CCP4i Anastassis Perrakis, Liz Potterton and Victor Lamzin 8. Vector-Search Methods in Molecular Replacement Carmen Álvarez-Rúa, Javier Borge and Santiago García-Granda 9. MAPSLICER: an interactive viewer for contoured map sections Peter Briggs 10. Protein Crystallography Specialist Users Group Meeting Pierre Rizkallah 11. Maximum-Likelihood Refinement of Atomic Models using Least-Squares Criterion P. Afonine, V.Y. Lunin and A. Urzhumtsev 12. CCP4i Chart Interface Paul Emsley 13. Efficient calculation of the exact matrix of the second derivatives Alexandre G. Urzhumtsev and Vladimir Y. Lunin 14. Reports from the Daresbury Protein Crystallography Data Collection Workshop Liz Duke and Jasveen Chugh 15. Improvement of noisy maps by bulk solvent correction A. Fokine and A. Urzhumtsev 16. Multiple rotation function L. Urzhumtseva & A. Urzhumtsev 17. An Open Source Multi-purpose Programming Environment for Macromolecular Crystallography Thomas Hamelryck and Morten Kjeldgaard 18. Recent improvements to Mosflm - version 6.11 Harry Powell 19. Recent CCP4BB Discussions Maria Turkenburg 20. CCP4/Max-INF Workshop on Refinement and Validation of Macromolecular Structure Eleanor Dodson Editor: Peter Briggs Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, UK NOTE: The CCP4 Newsletter is not a formal publication and permission to refer to or quote from the articles reproduced here must be referred to the authors. News from CCP4: March 2001 Peter Briggs, Martyn Winn, Sue Bailey, Alun Ashton, David Brown, Charles Ballard 1. Staff changes In some ways it is the end of an era for CCP4, with the announcement of two departures from the core CCP4 team based here at Daresbury. Colin Nave writes: ``Those who attended the CCP4 study weekend will remember that Sue Bailey will be taking up a new job at Berkeley, California in April. Sue's drive and organisational abilities have been a key factor in the growth of the CCP4 project over the past 8 years. At the same time she has managed a succesful research program at Daresbury, investigating the structure of DMSO reductase and other proteins. I have found it a pleasure working with her during her time at Daresbury. I am sure the CCP4 community will join me in wishing Sue and her family all the best in California.'' The DL staff would like to thank Sue for her invaluable contributions to the project and wish her all the best for the future. Also David Brown, the CCP4 administrative assistant, announced his intention to retire this coming summer. David has been with CCP4 for two years now and during that time has made valuable contributions to the overall running of the project - particularly in dealings with our commercial customers and also in the organisation of the annual Study Weekends. We are sorry to see him go but wish him a relaxing and enjoyable retirement. 2. Workshops and Conferences Since the last CCP4 newsletter almost a year ago there has been a large number of CCP4-related activities. Last July Alun Ashton, Peter Briggs and Harry Powell made a trip to the 50th Anniversary ACA Meeting in St. Pauls, Minnesota, where we had a stand in the exhibition, demonstrating CCP4 and MOSFLM, and were treated to some American hospitality! We had a great time meeting American users of the software, many of whom were only known to us previously as names on the bulletin board. From left to right: Katherine McAuley, Alun Ashton, Peter Briggs and Harry Powell at the ACA 2000 So we would like to thank everyone who came to visit the stand. We would also like to thank Katherine McAuley for helping out with demonstrations of the software, and to the ACA Council, who very kindly offered us the complementary exhibition booth. If you missed us then we will be back at the ACA again this summer, this time in Los Angeles - see the web page at http://www.hwi.buffalo.edu/ACA/ACA- Annual/LosAngeles/LosAngeles.html. Also last summer Martyn Winn, Charles Ballard and Harry Powell represented CCP4 at the ECM 19 meeting in Nancy last August (thanks to those who came to look at our posters). Martyn also presented recent developments in REFMAC at the Gordon Conference on Diffraction Methods in Molecular Biology held last July. More recently, the CCP4 Study Weekend 2001 took place in York in January, on the topic of "Molecular Replacement and its relatives". CCP4 would like to thank especially the scientific organisers - Jim Naismith (St-Andrews) and Kevin Cowtan (York) - and of course all the speakers. Alun Ashton, David Brown and Daresbury staff (Pat Broadhurst, Alison Mutch and Sue Waller) also played a vital role in making sure that things ran smoothly on the ground. The proceedings from the study weekend will be published later this year in Acta Cryst. D, but in the mean time Maria Turkenburg has compiled a useful set of associated links at http://www.ccp4.ac.uk/stwk01URLs.html This year the Study Weekend was flanked by a number of additional activities. The SRS PX Specialist User Group Meeting took place on the Thursday afternoon prior to the start of the workshop (see the report by Pierre Rizkallah), while on either side of the Study Weekend there was the CCP4/MAX-INF Refinement Workshop also in York (see Eleanor Dodson's report for more details). Finally on the Friday morning a short "Introduction to CCP4" session was held just before the start of the official Study Week programme. CCP4 staff and friends (Martyn Winn, Alun Ashton, Maria Turkenburg, Peter Briggs, and Harry Powell) presented material aimed at both new and existing users of the suite. We would like to thank those who attended (the hall looked quite full from the stage!) and hope that you found it useful. CCP4 also participated in the PX Data Collection Workshop held at Daresbury Laboratory at the start of February. Twenty students from labs around the UK attended the week-long event, which covered various aspects of protein crystallography and featured a number of hands-on practical sessions. (We would like to say particular thanks to Lisa Wright for bravely using the CCP4 graphical interface for her Molecular Replacement session!). We have two reports on the workshop in this newsletter, one by organiser Liz Duke and the other by workshop student Jasveen Chugh. Bringing us more-or-less up-to-date, Alun Ashton attended the recent ESRF High Throughput Structural Biology satellite meeting in Grenoble, presenting a poster on the developments within CCP4 in anticipation of high-throughput structure determination. CCP4 presence of some description is already planned at a number of forthcoming meetings, including: BCA Spring Meeting in Reading (April), the ECM, Krackaw (August; see http://www.ch.uj.edu.pl/ECM2001.htm), BCA Summer School in St. Andrews (September). Details of relevant courses and events can as always be found on the CCP4 "Courses" page at http://www.ccp4.ac.uk/ccp4course.html. 3. New Release 4.1 The end of January saw the release of version 4.1 of the CCP4 suite, followed shortly after by the patch release 4.1.1. As always the patch release is intended only to fix minor bugs in the release, and if you are already using 4.1 without any problems then we don't recommend you bothering to upgrade. The major changes from 4.0 to 4.1 are: · REFMAC5 This is a major new version of the refinement program which can now automatically prepare geometric restraints and identify disulphides, covalent bonds and cis- peptides prior to refinement (dispensing with PROTIN). Includes new libraries for nucleotides, sugars and some common ligands. A molecular SKETCHER is provided to create and modify monomer library entries. REFMAC5 also offers an improved bulk solvent correction and the option of refining TLS parameters. · MOSFLM 6.10 The data processing program MOSFLM is now included as part of the suite and will build automatically under the --with-x option of configure. On systems where this option is not supported, manual building of MOSFLM should still be possible. (For more news about MOSFLM, see Harry Powell's article in this newsletter.) The release also includes the following new programs: · ANISOANL: analyses of model anisotropic U values (see the article on ANISOANL in this newsletter) · CAVENV: calculate macromolecular cavities & envelopes · COMBAT: prepare data for input to SCALA (replacement for ROTAPREP) · DTREK2MTZ: converts d*trek scalemerge output to MTZ format · FFFEAR: fitting model fragments into electron density · MAPSLICER: interactive viewer for map sections (see the article on MAPSLICER) · ROTGEN: simulates X-ray diffraction rotation images Updates to the graphical user interface CCP4i: · Installation: CCP4i no longer requires Tcl/Tk to be built with a non-default flag. It is best run using the bltwish interpreter. · New and updated tasks, including: o Monomer Library Sketcher (for graphics display of monomers and interface to Libcheck and the monomer geometry libraries). o New interfaces to: BAVERAGE, CONTACT, FFFEAR, DMMULTI, DTREK2MTZ, SFTOOLS for SF analysis, SIGMAA, and WATERTIDY. Other highlights in 4.1 include: · New versions of MOLREP, RSPS (4.2), DM (2.1), SCALA (2.7.5), MAPMASK and MAPROT · The MTZ file format has been expanded to include dataset-specific cell and wavelength information · Updated xdl_view library (4.4) · Option to include the LAPACK linear algebra package using --with-lapack configure switch (See the article on LAPACK in CCP4 4.1.) Finally, we are once again making precompiled binaries of CCP4 4.1.1 available for a limited number of platforms (essentially, only those we have easy access to!): IRIX (o32- and n32-bit versions, prepared on IRIX6.5 R10k) and alpha (prepared on Digital UNIX V4.0F).
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