Minutes of Working Group 2 Meeting ---------------------------------- Wednesday 3rd October 2001, York University, York Present: Eleanor Dodson (Chairperson) York Alun Ashton Daresbury/CCP4 Charles Ballard Daresbury/CCP4 Peter Briggs Daresbury/CCP4 Kevin Cowtan York Paul Emsley Glasgow Paul Fyfe Bristol Sheila Glover Oxford Nicholas Keep Birkbeck Eugene Krissinel EBI/CCP4 Katherine McAuly Daresbury Stuart McNicholas York/CCP4 James Raftery Manchester Maria Turkenburg York/CCP4 Alexei Vagin York Jan White Sheffield Keith Wilson (friend of meeting) York Martyn Winn Daresbury/CCP4 Apologies: Phil Evans, Liz Potterton, Lindsay Sawyer, Ian Tickle, Rasmus Fogh, Neil Isaacs, Tadeusz Skarzynski, Maeri Howard-Eales, Peter Moody, Harry Powell, Vilmus Fulop, Christine Cardin. 1. Minutes of meeting of 6-6-01 and matters arising Chair The Chair would like to congratulate Peter Briggs on his minutes for the last meeting. 2. Introduction to new members of staff M.Winn The meeting was informed that administrative assistants position had been filled; Maeri Howard-Eales (m.howard-eales@ccp4.ac.uk) started in July. Stuart McNicholas has joined the molecular viewer project as a programmer. The second position remains vacant, L. Potterton and M. Noble are actively seeking a candidate. CCP4 is funding a Ph.D. student, Dan Zhou, with G.Murshudov. 3. Study Weekend 2002 K.Wilson Date Ð 4/5 January, 2002 Venue Ð York Topic - High-throughput Structure Determination Organisers Ð D.Stuart, K.Wilson, R.Esnouf The current timetable was outlined (http://www.ccp4.ac.uk/stwk/2002/prog.html) a. introduction b. target selection - 2 speakers have not replied c. protein expression d. crystallisation e. software - graphic and model building The study weekend dinner is to be held at York Racecourse again. A PX Specialist Users meeting is organised for the afternoon of Thursday 3 January (Pierre Rizkallah). The organisers have arranged a full timetable, which covers a wide range of topics. Due to this the length of many of the talks would be restricted to 20 minutes. A.Ashton indicated that there had already been 120-130 registrations, although this figure included few students. Working Group members were urged to advertise the study weekend to their students. E.Dodson asked if CCP4 was providing scholarships for a visiting Indian and Chinese student. The subject was to be raised with Working Group 1 and N.Isaacs [1]. Following confirmation CCP4 is to seek host institutions. 4. Development of CCP4 website to support off-site projects A.Ashton CCP4 online services have been added to the CCP4 website. These include CCP4 masterclasses (CCP4 talk), and archives of the ccp4bb. Working Group members were asked for ideas for talks and tutorials to be placed online. A.Ashton previewed plans to change the CCP4 group site into a CCP4 developers site. This would make the current development version available using CVSweb, and provide an online repository. E.Dodson asked about the mirroring of other Autostruct software. A. Ashton replied that this was not our responsibility, and that the current site points to the relevant pages. The developments were welcomed and endorsed. 5. Port of CCP4 to Mac OSX C.Ballard MacOSX will be a supported platform in the next release of CCP4. With the availability of g77 there are no outstanding problems with compiling the suite. Difficulties remain, however, in obtaining the subsidiary packages required. Non-standard packages required for compilation include the compilers, which are distributed separately from the operating system, and Xfree86. Currently static compilation is ruled out by the lack of a crt0.o. The situation is to be monitored. 6. Developments in the ccp4i project P.Briggs The next release of ccp4i is to be a minor revision, concentrating on continued refinement and bug squashing. Highlights include new interfaces (ACORN, OASIS,TLSANL,É), task consolidation (data importing), task installer, and mapslicer. Other ongoing projects: automatic test for consistent indexing in datasets when merging, the prototype hierarchical viewer for mtzfiles, and the extension of the MolRep task to use the AmoRe MR model database. CCP4 staff are liasing with H.Powell and G.Winter on the new Mosflm GUI. The Chair requested feedback from working group members on the usage of ccp4i. 7. Evaluation of AstexViewer P.Briggs P.Briggs intends to include AstexViewer in the next release of CCP4, but requires the final agreement of Mike Hartshorn. It was noted that contrary to standard CCP4 practise it might not be possible to include the source code. It was agreed that P.Briggs should continue to investigate the possibility of distributing AstexViewer, but that if a license could not be obtained by the next release then no further action was to be taken. 8. Next release of CCP4/ release and patch strategies P.Briggs The deadline for external developers was announced as 30 November, with an alpha release in Jan 2002, followed by a final release following a month later. New programs: BEAST, ACORN, WHATCHECK (ASTEXVIEWER). Gert Vriend has agreed to the release of WHATCHECK as part of CCP4. The code is autogenerated so there would be limited freedom to customise. It was felt that alignment program would be required as a front end for BEAST. The suite does not contain one at this juncture. E.Dodson suggested approaching Gerard Kleywegt about 6DLSQMAN (Uppsala), which is used in York. E.Krissinel pointed out that the mmdb libraries already contain many of the functions required for this alignment. It was agreed that E.Krissinel, E.Dodson (and Randy Read) should investigate the production of an mmdb based alignment program. Plans were announced for the use of source and binary patch files after the release of 4.2. This would allow users to easily update their version of CCP4, without having to download the full suite. This was felt to be a good idea. It was generally agreed that the CCP4 suite requires a more transparent configure procedure, preferably one that automatically tests for dependencies. Related to this J.White requested a list of requirements be placed on the web pages. P. Emsley and J.White are to look at these. 9. Plans for an intermediate library release M.Winn This will include new versions of routines for MTZ files, map files, coordinate files, parsing, etc,... It is planned to release much of the new libraries, particularly mmdb with associated programs, in 4.2 Whether the main suite will be made dependent upon the new libraries depends on developments between now and the release. Documentation of much of the libraries is still required. Minuted in the last working group meeting is the suggestion that CCP4 should investigate the use of cctbx. M.Winn reported symlib.c which uses a flat file format with spacegroups compatible with cctbx. The new library would be also be compatible with the new "symmetry tables". Some concern was expressed (S.Glover) about the phasing out of CCP4 spacegroup numbers. It was pointed out that these would be supported under the next release at least. K.Cowtan and M.Winn will continue to work on this. E.Dodson asked what information would be held in the "symops" file. K.Cowtan replied that it was planned to only store that information which could not be generated on the fly. E.Dodson requested that a human readable file also be produced. The need was noted for a library developers meeting. The date of this was not finalised. 10. New coordinate libraries - progress report E.Krissinel http://msd.ebi.ac.uk/~keb/cldoc Advances include the enhancement of editing tools for the coordinate hierarchy, and the incorporation of more high-level functionality such as the generation of symmetry mates. Along side this applications have been developed which use mmdb; NCONT contact hunting tool, and PDBCur PDB editing tool. Further projects include monomer libraries; functions for identifying residues and ligands from raw coordinate data. This is to work by building a structural graph. The graph library is currently under development. 11. Molecular Graphics project. S.McNicholas http://www.ysbl.york.ac.uk/~lizp/molgraphics.html A demo version of a prototype viewer was shown. L.Potterton and M.Noble have indicated to the Chair that a working demo will be available early in the new year. S.McNicholas has been working to link Python and Tcl to mmdb using SWIG. Problems identified include the lack of overloading in the scripting languages, the lack of pointers and that SWIG converts references to pointers. Stuart was confident that these problems had been overcome and that a full Python interface would be available by the end of the week. Python code interfacing to mmdb was shown. 12. Automation of data acquisition and processing C.Ballard http://www.dna.ac.uk The progress was broadly outlined. The automation of the strategy task is almost complete and it is expected that it will be installed on a beamline at the ESRF during the winter shutdown. 13. Date of next meeting During the 6/6/01 meeting it was agreed that the January 2002 Working Group meeting would be held later in the year at the BCA meeting in Sheffield. The suggested dates are 27 or 28 March. This was to be left to the local organiser, C.Cardin, to arrange. 14. Any Other Business Due to the later date of the Working Group 2 meeting it was agreed that suggestions for the 2003 study weekend would be made available on the WG2 mailing list. Current suggestions include Phasing (K.Cowtan) and model building[2]. A.Ashton noted that due to the early start of the Winter term at York University the 2003 study weekend would either have to be very early, moved to a different location, or held later in the year. M.Howard-Eales is investigating the possibilities. The Working Group members were asked to come up with ideas for crystallographic workshops that could be undertaken as part of MaxINF. M.Winn pointed out that there were relatively few users at the meeting, and that the current meeting was largely concerned with matters of interest to developers. It was asked if the format of Working Group 2 meetings should be changed to make them more useful to user groups[3]. This became a wider discussion of how to increase feedback from users. Ideas advanced included a user slot in the next meeting, an anonymous suggestion box on the web page, and a user forum at the study weekend. It was agreed that the user slot should be tried at the next meeting, and that web-based bug report page should be implemented[4]. S.Glover lead the meeting in congratulating E.Dodson on being awarded a Personal Chair at York University. It was minuted that G.Murshudov was to become a Senior Welcome Fellow from 1 November. Congratulations were expressed. [1] The scholarships have been approved in principle (8/10/01). N.Isaacs has sent letters to Prof. M.Vijayan at the Indian Institute of Sciences and Prof. Liang Dong-cai at the Academica Sinica asking for candidates. [2] N.Keep Ð suggestion for study weekend: building, refinement and interpretation at lower resolutions. [3] N.Keep Ð a useful addition to Working Group 2 meetings would be a talk on new software, if possible by the developer and a beta-tester. In the absence of this a meeting could be organised shortly before each major release where new software and upgrades to libraries could be described for the users. This could also incorporate presentations on the preliminary information for the following release. [4] (8/10/01) The bug report web page has been implemented.