Minutes from Working Group 2 Meeting 12th May 2004, Royal Society, London. _____________________________________________________________________ Present: Phil Evans(Chairperson) MRC LMB Alun Ashton DL/CCP4 Charles Ballard DL/CCP4 Geoff Battye MRC-LMB Peter Briggs DL/CCP4 Kevin Cowtan York Eleanor Dodson York Paul Emsley York Gwyndaf Evans DIAMOND Sheila Gover Oxford Maeri Howard Eales DL/CCP4 Eugene Krissinel EBI/CCP4 Katherine McAuley Diamond Airlie McCoy CIMR Pryank Patel DL/CCP4 Liz Potterton York Harry Powell MRC-LMB Tadeusz Skarzynski GlaxoSmithKline Norman Stein DL/CCP4 Jan White Sheffield University Martyn Winn DL/CCP4 Apologies: Stuart McNicholas, Keith Wilson, Ian Tickle, Nick Keep, Martyn Winn, Lindsay Sawyer, Martin Noble 1. Minutes from last WG2 meeting. Phil thanked Alun Ashton, who will be leaving CCP4 on the 23rd of May, for all his work for CCP4. Phil also thanked everyone involved with yesterday's release of 5.0. Minutes of meeting dated 20.1.04 were approved. 2. Study Weekend 2005 It was confirmed that SW 2005 would be held at the University of Reading on the 7th and 8th of January, with the conference dinner at Newbury Race Course. Questions were raised about whether this was too far away for the dinner. Gwyndaf discussed the scientific content and his thoughts as to how many speakers were needed. He reviewed the potential list of speakers for comments. Formal invitations and a preliminary program for the speakers should be sent out in June/July. It was agreed that Gwyndaf & Martin would produce a three or four page introduction to the meeting to be distributed at the beginning of the meeting. Questions or comments on SW can be sent to Gwyndaf at Gwyndaf.Evans@diamond.ac.uk or Martin at walsh@esrf.fr Gwyndaf also questioned whether we needed a keynote speech similar to the one given by Alwyn last year. It was generally agreed that this was not needed. It was also agreed that it was better to have fewer speakers with more time each. Tadeusz wondered whether someone should speak on Denzo. Phil also asked whether Gwyndaf would be speaking and he said that it was possible but depended on his work over the next month. There was also discussion on whether someone from Global Phasing would be speaking. This would be confirmed at a later date. 3. Date of the next meeting (to be held at York) 09 September 2004 4. Role of Working Group 2 and frequency of meetings This question arose from previous discussions with Keith Wilson, who is setting up more meetings with CCP4 staff and developers with an aim to have all developers more aware of what other people in the group are doing. Since WG2 is one of these meetings, Phil wanted to discuss the function of WG2. A: Phil said that it was originally a technical developers meeting but that it had become more a user's forum, and maybe it should be recognised formally as an opportunity for users and developers to discuss together what is new and what are the problems. B: It was also a forum to plan and oversee the Study Weekend. Charles asked for an overview of all of the different groups that are involved with the management of CCP4. Phil described the constitution of WG1, the Executive Committee (Colin Nave is the most recently appointed member of the executive committee) and WG2. Discussions were held on workshops and the possibility of having CCP4 visit sites for workshops and what was the best way to develop these. This should be discussed by WG1. Peter Briggs asked why those present had come to the meeting, what did they get from it. Phil said that members of CCP4 staff were generally asked to report on their current work at WG2, but this should only me necessary if they had something new to present. Conclusions: Tadeusz Skarzynski suggested that the role of WG2 should be publicised more, particularly to groups which did not send a representative to WG2 meetings. Liz Potterton suggested making the minutes of WG2 meetings public on the web Tadeusz suggested there should be a summary of each meeting and who is invited. Maeri will send Phil a copy of Keith's plans for meetings over the year. The frequency of WG2 meetings depends on frequency of developers' meetings. Phil suggested WG2 meetings in January and September. No firm decision can be made on this subject until the September meeting. Phil said that we should encourage groups to send a representative. This would encourage dialogue between users and developers. 5. Update on 5.0 Peter Briggs gave information on the status of 5.0. Released at 3.30pm on 11th May 2004. Binaries to follow shortly for Windows, Macintosh, Linux, Irix, OSF1 and Solaris. There was a description on the new items in 5.0. Liz Potterton asked about function of pdbcur. It is a manipulation tool for PDB files, but does not have all the functionality of pdbset. Eleanor wanted to know if there was information on where to download the extra programs needed to run certain tasks, such as Modeller and ClustalW. Answer: http://salilab.org/modeller/modeller.html ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ Phil asked whether the users had to send all 15 pages of the licence back. Maeri commented that people have sent just the last page with details on it, which is fine. Gwyndaf enquired about distributing software which used other licences. Kevin said that this was ok, as long as software did not include anything with a GPL-incompatible licence. Peter commented that our licence does not override other licences. Paul Emsley inquired if there was to be a graphical installer for Macintosh. Charles said yes. Phil has managed to get arp_warp 6.0 working with ccp4 version 5.0. In order to get it working, fix needs to be made to arp_warp.tcl. Phil will post information on how to get arp_warp 6.0 working with new ccp4 [Anastassis Perrakis has also posted this information]. 6. Conferences 2004 Maeri listed the conferences that CCP4 staff will be attending this year: the big 3 are - AsCA, ACA and ECM. It was mentioned that it was important to take advantage of conferences. Cost is factor in not having workshop at ECM. EJD to discuss with MDW on ECM issue, although probably too late to do anything at this stage. The timetable for the ACA workshop was also discussed. Charles asked if there was any more information about the possibility of workshops being organised in Asia. Phil suggested that the demand for that should come from the other end. 7. Molecular Graphics Project Liz said that there was a test version available. Bug reports to be sent by email. She asked if there were any subjects people want to raise. CCB asked about timescales about standalone release and merge into suite. Timescales were dependant on feedback. Tadeusz asked if there was any idea about the number of downloads. Liz replied that she was not pushed for download numbers. Would rather have close people downloading the program and giving feedback. 8. LIMS Alun Ashton was not sure what to report. Project has been successful. Chris is adding to project successfully. There was a discussion about the status of various grant applications and how this would have an impact on the LIMS project. Until the issues of grants are resolved, Alun will remain as Chris' mentor/advisor, his line management will be Martyn Winn / Colin Nave. Core Data model will be frozen in July, with a timescale for revisions. 9. CCP4 in BioXHIT Peter Briggs described the EU BioXHIT project and involvement by CCP4. The relevent sections are 4 and 5, data processing and structure determination, and databases and networking. Phil asked how this relates to CCP4's automation project. Not clear how effort gets divided up yet. Peter said that if somebody else has developed something similar, we would want to use that and use time on other efforts. 10. Pirate Kevin Cowtan described his new program pirate. First version released yesterday. Sorting out portability and licencing. Outperforms dm, Solomon and resolve on tests KC has run. Designed for automation, but version released is NOT automated. Version released forces people to put in certain information by hand, to enable people to understand what's going on and for more informative feedback. Next thing to do is NCS. Could just write in a dm-style NCS which would not be automated but would do good job. This would take 3 months. Kevin would like to reinvent NCS averaging and designed from ground up. Not ready for at least a year because of teaching commitments. Charles asked about a timescale for 1.0 release. Whenever 5.1 is released, then Pirate goes out in whatever state it is in. Kevin said that there is a gui for it which installs, need to install the gui module and copy binary to $CBIN directory. At present, binaries are for linux and OSX. 11. CCP4 automation project Charles Ballard talked about automation project. Whole room objected immediately to colour scheme of his slides (apart from Jan White). Introduced Norman Stein as recruited member of staff. An advisory (STAB) committee has been formed. Paul Emsley asked if Charles would be writing wrappers or changing programs? Charles replied that it would be a bit of both. 12. Mosflm Geoff Battye gave a brief update on mosflm status. Alpha-testing of new gui would take place at the end of June. A beta-release for interested people in September. Release after fixes made to beta. Harry Powell then gave a brief update. The latest release of mosflm came out in the recent 5.0 release. Will delay LMB release until everybody has 5.0 installed because it no longer runs with version 4.2.2 (this is 6.2.4 version of mosflm). Harry wants to look at images which Gideon Davies says index in denzo and not in mosflm. He now has version which runs on windows provided you have cygwin installed. Windows version on hold until Harry gets a visual C compiler. Paul Emsley asked about using MingW? Seems to work fine except for MAR images of any kind. Tadeusz asked about mosflm output. Were there any attempts to streamline output to make it user-friendly? Harry needs to know what he wants as output. 13. AOB Item from Airlie McCoy: there is no formal way of keeping unique reference number for people who have signed the licence so it can be cross-referenced with people using Phaser. Can everybody who has returned licence be given unique licence number? This is so Airlie can ask users to quote licence number when using phaser, since one of the licences associated with phaser is the ccp4 licence. Jan White asked if the extra programs used in the suite can be made available from the same download site as CCP4? Eleanor said probably not. Liz suggested that perhaps we could provide pages and links to these other packages. Action point: Maeri and Airlie to clarify requirements for Phaser. Harry: software patents in front of EU parliament. Act went in front and had so many amendments attached to it. Now back in original form. Check on The Registry. Write to your MEP.