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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 41 Fall 2002 Contents CCP4 News 1. News from CCP4. Alun Ashton, Charles Ballard, Peter Briggs, Maeri Howard-Eales, Pryank Patel and Martyn Winn. 2. Developments with CCP4i: October 2002. Peter Briggs. 3. Developments with the CCP4 library II. Martyn Winn, Charles Ballard and Eugene Krissinel. General News 4. BioMed College at Daresbury. Gareth Jones. Software 5. Handling reflection data using the Clipper libraries. Kevin Cowtan, Department of Chemistry, University of York, UK. Theory and Techniques 6. Atomic displacement in incomplete models caused by optimisation of crystallographic criteria. P.V Afonine, Université Henri Poincaré, Nancy, France, Centre Charles Hermite, LORIA, Villers-lès-Nancy, France. 7. Modelling of bond electron density by Gaussian scatters at subatomic resolution. P. Afonine(1,2), V. Pichon-Pesme(1), N. Muzet(1), C. Jelsh(1), C Lecomte(1) and A. Urzhumtsev(1), (1) Université Henri Poincaré, Nancy, France, (2) Centre Charles Hermite, LORIA, Villers-lès-Nancy, France. 8. Bulk-solvent correction for use with the CCP4 version of AMoRe. Guido Capitani(1) and Andrei Fokine(2), (1) University of Zürich, Switzerland, (2) Université Henry Poincaré, Nancy, France. 9. Variation of solvent density and low-resolution ab initio phasing. Andrei Fokine, Université Henry Poincaré, Nancy, France. 10. Retrieval of lost reflections in high resolution Fourier syntheses by 'soft' solvent flattening. Natalia L. Lunina(1), Vladimir Y. Lunin(1) and Alberto D. Podjarny(2), (1) Russian Academy of Sciences, Russia, (2) CU Strasbourg, France. Bulletin Board 11. Summaries. html Maria Turkenburg, University of York, York, UK. Editors: Charles Ballard and Maeri Howard-Eales 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: Autumn 2002 Charles Ballard, Martyn Winn, Alun Ashton, Peter Briggs, Maeri Howard Eales, Pryank Patel 1. CCP4 study weekend The 2003 CCP4 study weekend is on "Experimental Phasing" and takes place on the 3rd and 4th of January at York University. The scientific organisers are Neil McDonald (Cancer Research UK) and Airlie McCoy (Cambridge, UK). Invited speakers include: Gérard Bricogne(Global Phasing, UK) Ditlev Brodersen (MRC, UK) Zbigniew Dauter (Brookhaven, USA) Phil Evans(MRC, UK) Eleanor Dodson(York, UK) Gwyndaf Evans(Global Phasing, UK) Joe Ferrara (Rigaku/Molecular Structure Corp,USA) Elspeth Garman (Oxford, UK) Ana González (Stanford, USA) Ralf Grosse-Kuntsleve (Berkeley) Simon Parsons,(Edinburgh, UK) Michael Quillin (Oregon, USA) Raimond Ravelli (EMBL, France) Randy Read (MRC, UK) Gabby Rudenko (Texas, USA) Thomas Schneider (Göttingen, Germany) Bi-Cheng Wang (Georgia, USA) Again CCP4 will be running the highly regarded “Introduction to CCP4” mini-workshop on the Friday morning 9-10:30. The topics to be covered will include · General introduction to CCP4 · CCP4 Road Maps · Where to find help on CCP4 · What's New in CCP4? Also, there will be a Protein Crystallography Specialist Users Group meeting on the Thursday afternoon, starting at 14:30. The Proceeedings of the 2002 CCP4 Study Weekend on "High-throughput Structure Determination" are available in Acta Crystallographica Section D Volume 58, Part 11 (November 2002). 2. Workshops and Conferences The CCP4 conference roadshow for 2002 had stands at the XIX Congress and General Assembly of the IUCr in Geneva, Switzerland, and at the American Crystallographic Association annual meeting in San Antonio, Texas. In August CCP4 staff Charles Ballard and Peter Briggs along with MOSFLM expert Harry Powell (now a regular fixture at these events) travelled to the beautiful city of Geneva for the XIX IUCr congress. As usual we manned the CCP4 stand in the commercial exhibition and offered demos and tutorials of the software to an unsuspecting public. (We were also pleased to see the ab initio phasing program ACORN getting plenty of exposure, both in Michael Wolfson's opening lecture and Yao Jia-xing's talk in the scientific sessions.) We enjoyed the conference and the CCP4 staff with the PDB at Geneva city (especially its amazingly efficient public transport!) and we'd like to thank all those people who took the time to come and talk to us - it's always a pleasure to meet our users face-to-face and hear your comments. Prior to the ACA an “Introduction to CCP4” one-day workshop was held. This was a great success, being attended by more than 80 people. CCP4 would like to extend it's thanks to the speakers, Harry Powell, Roberto Steiner and our own Alun Ashton. Following this success there will be a one-day workshop on July 26thorganised in conjunction with the 2003 Annual Meeting of the ACA at Cincinnati, July 26-31. Data processing and scaling with Mosflm and CCP4 ACA Annual Meeting, Cincinnati, 26 July, Organiser Harry Powell The package distributed by CCP4 includes programs for all aspects of protein crystallography up to the model building stage. Following a short introduction to the suite, this workshop will concentrate on integration and scaling datasets with Mosflm and SCALA. Basic processing of routine datasets will be followed by detailed analysis of the programs' output and treatment of more demanding experiments. While new users of the programs may benefit, this is aimed at protein crystallographers with some experience of data processing who may want to develop their skill in using these programs. There will be presentations by CCP4 staff and developers as well as the opportunity for informal group discussions during the workshop. 3. Release of CCP4 4.2 On April 30 CCP4 release version 4.2 of the suite. This release included the follwing new applications: ACORN ab initio procedure for the determination of protein structure at atomic resolution (Yao Jia-Xing) BEAST Brute-force molecular replacement with Ensemble Average Statistics, Maximum likelihood-based molecular replacement (Randy Read) PROFESSS determination of NCS operators from heavy atoms (Kevin Cowtan) ROTAMER list amino acids whose side chain torsion angles deviate from Richardson's Penultimate Rotamer Library (Dirk Kostrewa) ASTEXVIEWER Java application for viewing proteins, ligands and electron density maps (Mike Hartshorn) plus others.... Also new versions of REFMAC5 (5.1.19), MOSFLM (6.2.1), DYNDOM(1.2), FFFEAR(1.9), MOLREP(7.3) and SCALA (3.1.4). Updates to the graphical user interface CCP4i: · New and updated tasks, including: o New interfaces to: ACORN, BEAST, OASIS, ANISOANL, TLSANL, PHISTATS, PROFESSS o New stand-alone task in Coordinate Utilities to import and edit a protein sequence. o An explicit "Structure Factors for Deposition" task to encourage you to deposit your data! · ARP/wARP: stand-alone interface has been withdrawn - get the latest ARP/wARP suite and CCP4i interface from http://www.arp-warp.org/ · Map sections can be viewed with MAPSLICER, and this can be set as the default viewer in the Preferences. · Configuration: The task lists can be customised using the "Edit Modules File" task under the "System Admin" menu. · Install New Task: substantially revised version allows install, uninstall and export of new tasks. Other highlights in 4.2 include: · Compliation for Mac OSX using Darwin configure switch. · Compilation of the LAPACK linear algebra package is now the default as REFMAC, SCALA and BEAST now depend on it. In extremis, there is a --disable-lapack configure switch. · New library pxxml.f for writing XML files. These routines are used by ALMN, MATTHEWS_COEF and PEAKMAX. Plus many, many minor changes.... More recently version 4.2.1 was released on July 15 and 4.2.2 on November 25. Binaries are available for IRIX, linux (intel), OSF, SunOS, Mac OSX and Windows. 4. Other news Graeme Winter, who previously worked on the updating of the Mosflm GUI and server, has joined Daresbury Laboratory as part of the e-HTPX project. His brief is to work on the automation of protein structural solution. The aim of the e-HTPX project is to unify the procedures of protein structure determination into a single all encompassing interface from which users can initiate, plan, direct and document their experiment either locally or remotely from a desktop computer. More information is available at www.e-htpx.ac.uk. Developments with CCP4i: October 2002 Peter Briggs, Pryank Patel, Alun Ashton, Charles Ballard, Liz Potterton*, Maria Turkenburg*, Martyn Winn CCP4, Daresbury Laboratory, Warrington WA4 4AD, UK *Structural Biology Laboratory, Department of Chemistry, University of York Y010 5YW, UK Introduction CCP4i is the CCP4 graphical user interface. The last officially released version of the interface was 1.3.8, included as part of CCP4 4.2.1. This article outlines the major changes in 1.3.8 against the previous version of CCP4i, and looks ahead to some of the future developments planned for the next release and beyond. Changes in CCP4i 1.3.8 Many of the new and updated features in the current version of CCP4i were previewed in the previous newsletter (issue 40 March 2002). As well as a number of relatively minor changes to fix bugs and consolidate earlier changes, there were a number of new and updated task interfaces, reflecting changes and additions to the suite in release 4.2. New Interfaces These include interfaces for CCP4 programs ANISOANL, TLSANL and OASIS, as well as interfaces for the major new programs in 4.2: ACORN (ab initio procedure for the determination of protein structure at atomic resolution), BEAST (maximum-likelihood molecular replacement program), PROFESSS (determination of NCS operators from heavy atom substructure) and ROTAMER (comparison of atomic coordinates against Richardson's Penultimate Rotamer Library). In addition, the GET_PROT interface (now renamed SAPHIRE) is a CCP4i-only application which allows the user to download and edit protein sequence files accessed either from the EBI or from a local file.
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