Minutes of the Working Group 2 Meeting -------------------------------------- Wednesday June 6th 2001, Birkbeck College London ------------------------------------------------ Present: Phil Evans (Chairman) MRC, Cambridge Eleanor Dodson York Eugene Krissinel EBI/CCP4 Peter Moody Leicester Nicholas Keep Birkbeck Jan White Sheffield Alexei Vagin York Ian Tickle Astex Sheila Gover Oxford Paul Fyfe Bristol Robert Esnouf Oxford Christine Cardin Reading Harry Powell Cambridge Neil Isaacs Glasgow Charles Ballard Daresbury/CCP4 Alun Ashton Daresbury/CCP4 Peter Briggs Daresbury/CCP4 Martyn Winn Daresbury/CCP4 David Brown Daresbury/CCP4 Michael Roberts St Georges Medical School Tadeusz Skarzynski Glaxo Wellcome Liz Potterton York/CCP4 Rasmus Fogh CCPn Apologies: Yao Jia-xing, Keith Wilson, Dave Stuart, Lindsay Sawyer, Quan Hao, James Raftery 1) Minutes of meeting of 24-1-01 and matters arising. Chairman - The names of Eugene Krissinel (item 6) and Mike Hartshorn (item 8) were mis-spelt. - Item 11: the minutes gave the impression that the chairman alone was thanking Sue Bailey for her contribution to CCP4. In fact his thanks were on behalf of all of WG2. - Item 7: Kevin now says he is happy with the new CCP4 licence with respect to libraries - although it is not GPL (since there is a requirement that any changes need to be reported back to the community), the wording is now vague enough to be GPL compatible. 2) Study Weekend 2002 4 - 5 January 2002 Confirmed as York University Date - 4-5 January 2002 Venue - York Univeristy Topic - High-throughput Structure Determination Organisers - D.Stuart/ K. Wilson/ R. Esnouf Robert Esnouf presented the current provisional timetable and list of speakers for the scientific sessions. Provisional programme distributed showing 11 keynote speakers had accepted and replies awaited from 4 others. The format of Session 5 would be reviewed following discussion and it was agreed that a CCP4 talk on automation should be included in Session 4. Speakers should be given the topic/theme for their talk to avoid duplication or overlaps within sessions. Alun asked for feedback on the CCP4 mini-Workshop held on the Friday morning before last Study weekend and received very favourable comments. Recommended for a repeat next year and details included in the poster. The student bursary would be retained at the cost of one night's accommodation and the fee. Alun read a report from Jim Naismith of last years meeting including a recommendation to avoid inviting speakers again who had been habitual offenders at not producing a contribution to the proceedings. Thanks were given to Kevin for the valued contribution to the organisation - a gesture that Alun and the Chairman extended to include Jim for the excellent work they had done. Robert would provide Alun/David with details of the confirmed speakers to enable formal invites to be mailed. 3) Staff changes: progress on replacements for Sue Bailey and David Brown Martyn reported that 60 applications have been received for the administrative assistant's post, to replace David Brown. The job description is the same but raised from 50% to 75% time. The quality of applications has been very high. Interviews are to be held in a couple of weeks time, with the appointee starting in August. [Since this meeting a person has been appointed and will start on 9th July.] A new post of "CCP4 Project Manager" is to be advertised soon. This will replace Sue Bailey's post as CCP4 secretary and be raised from 50% time to 100%. Currently the recruitment is being processed by DL admin and it was hoped to hold interviews in July/August. The post is entirely management with no research component, and is not a research opportunity. Ideally the appointee should have management experience, though scientific programming experience would also be useful. Phil encouraged WG2 members to bring the post to the attention of interested colleagues. [NB: The advert for Project Manager has since been e-mailed separately both to WG2 members and to CCP4bb.] 4) Release of suite for NT Alun reported that after the NT release a couple of weeks ago there had been over 250 downloads - so far there have been few problem reports, most of these under Windows 98. The NT release seems to have created interest in porting CCP4 generally - there are now reports of the X-windows programs working under NT using the GNU Cygnus compilers. (Cygnus also offers a unix-like scripting environment under NT which might be useful for those who prefer scripts to the gui.) A second NT release is scheduled for this week. Harry: an NT version of MOSFLM is not yet available; this should become possible in the next 11 months - see item 9. Phil: asked about porting CCP4 to MAC-OS10. Charles volunteered to investigate this. 5) Transfer of CCP4i project to Daresbury and future plans Pete reported that following the release of CCP4 4.1.1, the CCP4i project had been transfered from Liz to DL, with Pete as Project Coordinator and Liz acting as consultant. All the DL staff are involved in maintainance and development. There are new CCP4i webpages accessible from the main CCP4 site, and CCP4i problems are listed on the standard CCP4 problems pages. Problems can be reported to either ccp4gui@ccp4.ac.uk, or the main CCP4 e-mail. Current developments were outlined: a pilot automation project; improvements for installing non-CCP4 tasks; additions to the functionality of loggraph; improvements to the project management utilities; development of a hierarchical viewer for reflection data, to tie into Clipper and CMTZ; development of the MapSlicer utility; new task interfaces (OASIS, ACORN and surface analysis progs). CCP4 staff are liaising with Harry and Graeme Winter to make the new MOSFLM CCP4i-compatible. DL staff are making visits to academic groups to demonstrate CCP4i and the suite (already visited Leicester, Manchester and Warwick). Finally there are notes available on the web from the CCP4i programmers workshop which was held in York at the start of April. This could be repeated if there is sufficient interest. 6) Plans for an intermediate library release Martyn: the twin motivations behind revising the CCP4 libraries are: 1. to reflect the developments in data formats e.g. the crystal/dataset/column hierarchy in MTZ 2. to ease linking into other languages e.g. Python, Java, Tcl Martyn has been revising MTZlib in C, and this is already used for the MTZ I/O in Clipper. There is also a Fortran interface to replicate the existing MTZlib, so that existing programs do not need to be rewritten. Charles is working on a C MapLib, also with a complete Fortran interface. There is also a new library.c which is callable from C, and C parser routines. The plan is to release these together with Eugene's coordinate libraries (but not Clipper) as a new CCP4 library in Autumn. This will be advertised to all users, not just developers. People can then use them to write new applications. The ultimate aim is to migrate the suite from Fortran to C. Regarding maps, it was suggested that "NaN"s/magic numbers could be used to allow storage of the unique ASU in a map. Eleanor suggested these could be used in EM "maps" to signify "nothing recorded at this position". She also suggested extensions to accommodate the requirements of the EM community, e.g. storing the phase origin. Martyn commented that CCP4 are happy to do this but the EM'ers have not yet been very active in discussing possible changes. A general point is to try and make the library components more "stand-alone" i.e. so that developers who only want MTZ functionality don't need install the whole CCP4 library. Kevin pointed out that American developers are particularly keen to have MTZ in C. It was suggested that CCP4 should investigate using Ralf Grosse-Kunstleve's symmetry libraries, instead of rewriting our own. Possible problems here are the license conditions, and the extreme form of C++ that it is written in; the advantages are standardisation of spacegroups and saving CCP4 developers some work. 7) New coordinate libraries - progress report Eugene reported that the development of the atom selection tools within the libraries is now finished, with approximately 20 functions allowing flexible selection of atoms, residues, chains and so on, plus logical operations (AND, OR, ...) between selections. There are two selection "languages" - direct specification of chains, residues, atoms, or a "Unix-directory"-like syntax (/chain/residue/atom) which includes wild cards and commas for lists. Selections on spatial positions (sphere, slab) are also possible. Also now developed are "contact-seeking" functions - these find contacts between a single atom and a set of atoms, or between two sets of atoms. Currently he is engaged in general debugging and writing documentation. Documentation is in XML, but has been translated into HTML and posted on his website. The documentation for the Fortran interface is now complete. Future plans are to enable checking of residues against the monomer libraries, and to write Fortran interfaces for the selection tools. It was suggested that it wasn't worth doing the latter work, it would be better for new applications to be developed in C. It was suggested that Eugene discuss with Garib the possibility of introducing his libraries into REFMAC5, particularly selection and contact-seeking functions. 8) 3d graphical viewer project Liz reported that two programmers have now been selected for the project, and should be starting sometime in August. One is a quantum chemist, the other is a computer scientist, but both have already worked in academic groups producing distributed software for distribution. One post will be based in York, the other in Oxford working with Martin Noble on the graphical libraries. The next step is to discuss how the viewer will look and work - already discussion has begun on the 3d mailing list, and a meeting will be held on 14th June, web pages will summarise the discussions and encourage more widespread input. Liz will publicise the webpages when available, and requests feedback and comments from everyone when this happens. 9) Automation of data acquisition and processing Harry outlined the ideas behind automation of MOSFLM and data processing - a central MOSFLM process will communicate with its graphical interface and other programs via TCP/IP sockets. A new programmer (Graeme Winter) is now employed to develop the MOSFLM gui - he has already visited the CCP4 programmers at DL, and is currently looking at how to use sockets. He will be using the CCP4i toolkit, liaising with Pete regarding any necessary extensions that are required, and to make the MOSFLM gui CCP4i-compatible. The MOSFLM gui will provide a general diffraction image viewer, which could be used to replace some of the CCP4 X-windows programs. A meeting will be taking place in Grenoble with the DL and ESRF beamline people, regarding the automation of communications between the collection and processing components. An expert system will use output from MOSFLM to determine the data collection strategy used by the data collection software. Both the collection and expert system components will be developed by the individual synchrotrons. The current version of MOSFLM already incorporates a degree of automation - all MOSFLM needs are the directory and image names, then it can autoindex, postrefine and integrate in background. This works with good images, and sometimes with bad ones - Hary asked for people to try it out and send him comments. Some of the features are in 6.01, all are definitely in 6.11. 10) ACORN Eleanor: ACORN is Yao's program for ab initio phasing from atomic resolution data. It is quick and not limited by the protein size. It is similar to SHELX and ShakeNBake - it takes a starting map and performs density modification rather than peak picking - it seems to work very well and has solved large proteins from single atoms. ACORN was originally developed as a BBSRC research project but is now being funded by CCP4 and is being brought into the suite for the next release. Currently it is distributed from the York ftp site for people to download and test. Alun added that there is a Makefile for ACORN available from the CCP4 ftp site. Yao wants to alter the density modification to enable the program to work at lower resolution (currently the limit is 1.2-1.3A), and would like to use it for finding heavy atom positions. Eleanor presented some results from running ACORN and commented that it seems to work more automatically than RANTAN (input is simpler and program doesn't get "stuck in a rut") and is faster. Maria (Turkenburg) is writing a CCP4i interface for the program. 11) Report on evaluation of AstexViewer An evaluation licence has been obtained from Mike Hartshorn, to allow CCP4 staff to evaluate his 3d molecular viewer program ("AstexViewer"), with a view to including it in some form in the next release. The viewer can display multiple structures and maps, allows rotations and "zooms" of the view (which can be dumped as a gif). Each map can be contoured at three levels, there are limited atom selection capabilities, and symmetry-related atoms can be displayed. It has no building or modelling capabilities. The viewer can be run as a standalone application or as an applet embedded in a html file. Since it is written in Java, in principle it should be extremely portable, however there are some portability issues which still need to be resolved. There may also be some issues with the speed of the viewer running on certain systems. It was pointed out that although CCP4 would get the source code, it was possible that we would only be allowed to distribute the compiled Java bytecode. WG2 felt that this would be an acceptable condition. Evaluation of the viewer continues. 12) Possibility of holding WG2 meeting at Nottingham BCA meeting The next BCA meeting is 28th March 2002 in Nottingham, and Peter Moody requested that a WG2 meeting could be held at the same time. He argued that CCP4 would have an opportunity to interact with a wider crystallographic community (not just biologists), at the same hopefully increasing the attendance of the meeting. A similar arrangement was made in 1998 when a WG2 meeting was tagged on the end of the St. Andrews BCA meeting. Chris Cardin, Peter and Harry Powell are involved with the BCA this year so it should be possible to avoid WG2 clashing with the biological sessions. Martyn wondered if having WG2 at the end of March was too soon after the January meeting. It was argued that the main point of the January was to start the ball rolling with organising the next Study Weekend. One possibility would be to announce WG1's decision to WG2 members via e-mail instead of meeting in January. Phil mentioned that there had also been prosposals for a CCP4 satellite workshop aimed at students attending the BCA, to "add value" to the meeting and hopefully attract more students. It was reported that the BCA would prefer CCP4 to providing additional funds instead, for example in the form of student bursaries. This was not acceptable to CCP4 (exec?). It was commented that one problem is that the meeting is expensive for students - Chris and Harry: next year it is likely that the BCA will waive the registration fees for students (and possibly postdocs), and that the BCA bursaries will be more generous but fewer in number. 13) Date of next meeting The next WG2 meeting is scheduled for October 3rd at York University. 14) AOB David Brown is retiring from the post of CCP4 administrative assistant at the end of June. There was a presentation on behalf of Working Group 2 and the chairman thanked David on behalf of CCP4 and the WG2 members for his contribution to the project. ___________________________________________________________________________