The WG1 Meeting was held at 9.00 - 10.45 on Sunday 4 January 2009 in Conference
Suite 4 a/b in the Nottingham Conference Centre
Jim Naismith (St. Andrews – Chair) Kevin Cowtan (York) Keith Wilson (York - Secretary) Adrian Lapthorn (Glasgow) Lindsay Sawyer (Edinburgh) Tadeusz Skarzynski (GSK) Garry Taylor (St Andrews) Mark Roe (ICR)
Phil Evans (MRC-LMB) Eleanor Dodson (York) John Helliwell (Manchester) David Stuart (Oxford) Leo Brady (Bristol) Andrew Leslie (MRC-LMB) Elspeth Garman (Oxford) Jenny Littlechild (Exeter) Frank von Delft (Oxford) Arwen Pearson (Leeds) Neil Isaacs (Glasgow) Tom Edwards (Leeds) Andrea Hadfield (Bristol) Thomas Sorensen (DLS) Vilmos Fulop (Warwick) Ralf Flaig (DLS)
Peter Moody (Leicester) Charles Ballard (STFC) Kate Brown (Imperial) Martyn Winn (STFC) Nicholas Keep (Birkbeck) Chris Morris (STFC) Richard Pauptit (AstraZeneca)
Apologies David Rice, Simon Phillips
1 Minutes of previous meeting were accepted. These had been circulated the previous January and were available on the web (http://www.ccp4.ac.uk/wg).
2 Matters arising: None not covered elsewhere.
3 Chairs report (Appendix 1)
The meeting recorded thanks to Randy Read and Gerard Kleywegt for organising such a successful meeting last year.
The meeting recorded thanks to Clemens Vonrhein (Global Phasing), Arwen Pearson (Leeds) and Elspeth Garman (Oxford) for undertaking to organise this meeting. Thanks also to Shirley Miller Damian, Tracey and Laura for their help with the organisation. XXX Surnames please
WG1 noted its thanks to the core staff Martyn Winn, Charles Ballard, Ronan Keenan, Norman Stein, Graeme Winter, Peter Briggs & Francois Remarcle. WG1 wished Graeme, Peter & Francois well in their new positions.
WG1 was pleased to note the release of V6.1, although expressed its desire to make sure the suite keeps pace with developments in component programs.
WG1 was pleased the grant was renewed. It made clear its desire to continue to seek research council support. WG1 thanked all those who contributed to the grant.
WG1 agreed a rise of 500 GBP for a full licence from Jan 2010 (approx 5%), with a pro-rata increase for the subsidiary license
WG1 discussed the state of the suite at length. While pleased with the progress, it was keen to see further improvements across the board. PHENIX has proven a spur to development. WG1 agreed that support for Irix could be dropped and suggested that only the main flavours of linux were supported. WG1 requested that a mock up of the new GUI be presented by Liz Potterton at the next WG1 meeting, and that she undertake visits to academic and commercial organisations to gather requirements and feedback. Several institutions expressed interest in hosting these sessions.
WG1 expressed its desire to see outreach targeted to students and new entrants into MX within the UK. There was no great desire to become a sponsoring organisation. Those involved in organising such activities are greatly appreciated by the whole community.
WG1 expressed its support for the move to RAL but noted its concern over the effects on the suite.
Kevin Cowtan left the room at this point.
There was a wide ranging discussion of Kevin Cowtan’s position with respect to future CCP4 funding. The following points were agreed
(1) Kevin Cowtan has been and is an outstanding scientific programmer
(2) CCP4 in particular has benefitted enormously from his selfless commitment to share the
fruits of his work
(3) His intellectual contribution to the grant was recognised, the new programs he is developing
are world leading.
(4) WG1 unanimously approved the executive proposal that CCP4 make a deferred offer of a
five year CCP4 fellowship to Kevin Cowtan.
(5) In making this offer, WG1 explicitly accepted that honouring this commitment in 4.6 years
time could lead to other projects being cancelled.
(6) WG1 therefore binds any future CCP4 Executive to honour the commitment to Kevin,
except and unless CCP4 has collapsed.
(7) WG1 required the Chair to notify York of this decision and to confirm with Kevin that York
will now guarantee Kevin a permanent underwritten position.
4 Managers report
1. Finance. KSW asked CB to report on the current financial status. With the usual caveats and
additional uncertainty causes by moving away from the direct invoicing of companies, the
balance sheet looks healthy, with an underspend predicted for this financial year (FY). This
would be, as much as possible transferred to next FY, which would leave funds to fund an
additional position. As yet the credit crunch has not effected the income, two companies having
cancelled licenses, but two new companies being taken onto the books. KSW thanked CB for
his excellent work on the finances and for overseeing the relocation packages. 2. The mechanics of the move to RAL were discussed at length together with their impact on
staffing levels. A number of core staff had left or chosen not to relocate. WG1 expressed
dissatisfaction that there would be a hiatus in staff levels at this crucial time. Particularly as the
new grant was about to start and the need for the new gui pressing. Whilst understanding the
frustration, the Chair and Manager felt that the circumstances are such that there was no easier
solution. However, they welcomed the offer from Frank Von Delft to host a gui programmer in
Oxford if such a person is appointed in advance of the research complex being completed. KSW informed WG1 about the establishment of a number of Working Parties (WPs) which report directly to the Executive at the biannual developers meetings. A corrected list of the WPs together with their reports for the previous 6 months for the November 2008 meeting will be sent to WG1 in January 2009. Individual activity reports as in previous years were felt to be unnecessary given these WPs.
Member of Executive
Peter Moody was proposed by Nick Keep
Alun Ashton (absent) was proposed by Andrew Leslie
Peter left the room. After a very close vote, Peter was elected to the Executive. WG1 was pleased that two such strong candidates stood for the post. (The current Executive did not vote)
Peter returned to the room.
Jim Naismith left the room.
After discussion of WG1, Jim Naismith returned.
WG1 requested Jim Naismith stay for one final year to ensure handover and he thanked WG1 for their confidence and agreed.
Two candidates were proposed for Chair designate
Keith Wilson was proposed by Yvonne Jones
Martin Noble (absent) by Elspeth Garman
Keith left the room. The current chair summarised the contributions of both to the grant and to CCP4.
There was considered discussion of the strengths of the two candidates. The meeting felt both were excellent choices and either would take CCP4 forward.
The Chair did not vote but the remainder of the Executive did.
Martin Noble was elected to the post of Chair designate. WG1 felt expressed its thanks to both candidates for standing and acknowledged their contribution to CCP4 over the years. Martin will become Chair at the January 2010 meeting.
The Executive is now
Randy Read co-opted
Garib Murshudov co-opted
Eleanor Dodson co-opted
Kevin Cowtan co-opted
Keith Wilson Manager, ex-officio
Simon Phillips elected, 1 year remaining
David Rice elected, 2 years remaining
Peter Moody, 3 years remaining
Phil Evans elected WG2, ex-officio
Martin Noble, chair designate (Jan 2010)
Jim Naismith, elected Chair WG1, 1 year remaining
6 Next Study Weekend
This will be at Nottingham again, and back to the traditional Thurs/Fri/Sat. Suggestions on topics to Phil Evans soon please.
There was none.
Appendix 1 Chairman’s report on behalf of the Executive
1 Study weekend
We thank Randy Read and Gerard Kleywegt for organising such a successful meeting on "Low
Resolution Structure Determination and Validation".
We look forward to this years study weekend organised by Clemens Vonrhein (Global Phasing), Arwen Pearson (Leeds) and Elspeth Garman (Oxford) on the topic “Experimental Phasing and
Radiation Damage”. The final attendance is 320
2 State of the suite
I would like to record the thanks of the entire community to the core CCP4 staff, Martyn, Charles, Ronan, Norman, Graeme, Peter & Francois. The suite continues to expand in usefulness, reliability and uptake. We currently derive an external income of approximately ?882K per annum from around 130 licences. The more robust regime we implemented for monitoring the projects, where we measure progress against milestones, is bedding in. We will hold a full meeting of developers in
thApril (15-17 at The Cosener’s House), a smaller follow up one day meeting in the autumn will review reports from the various working parties.
The release of CCP4 v6.1 is a major addition to functionality. I will highlight some specific programs below. As part of this release we have extended and overhauled our testing procedures, we are finding and fixing bugs before they go out the community.
We have said a sad goodbye to Peter Briggs, Maeri Howard and Francois Remacle this year. We were extremely sorry to see them go but we thank them for their contributions over a number of years and wish them well in their future careers.
3 BBSRC Grant
The grant was funded in full. The referees comments were glowing and we are grateful to BBSRC for their farsighted support of CCP4. As a community we need to recognise the hard work done by the people who put the grant together. The list of honour is very long but special thanks to Kevin Cowtan, Harry Powell, Andrew Leslie, Charles Ballard, Martyn Winn, Martin Noble, Randy Read, Eleanor Dodson, Peter Briggs and Phil Evans.
As Peter Briggs has left CCP4, Liz Potterton is now overseeing the GUI. More on the move to Diamond and new appointments below.
The final report on the last grant has been submitted.
The Executive is currently
Randy Read co-opted
Garib Murshudov co-opted
Martin Noble co-opted
Eleanor Dodson co-opted
Kevin Cowtan co-opted
Keith Wilson Manager, ex-officio
Simon Phillips elected, 1 year remaining
David Rice elected, 2 years remaining
Phil Evans elected WG2, ex-officio
Jim Naismith, elected Chair WG1, 0 years remaining
One additional elected representative is required this year.
An election is required for the new chair.
The community owes the co-opted and elected members of the Executive (Eleanor, Keith, Randy, Martin, Simon, David, Garib, Kevin and Phil) together with Martyn Winn and Charles Ballard a thank you.
There was no increase in the licence fee last year. The Executive suggests we consider a 5% increase for Jan 2010 to keep pace with inflation.
Keith Wilson (CCP4 manager) will present a more detailed overview of finances, posts and commitments.
The suite is financially stable, provided commercial income holds up, and we do not foresee any contraction. We are, however, acutely aware of the need to invest properly, review projects and re-jig priorities where necessary.
6 Major projects
(6.1) The graphics viewers: Paul Emsley, the author of COOT, is the first CCP4 fellow and is based at Oxford. COOT 0.5 is released and widely taken up. It includes Ramachandran refinement restraints, "fixed atoms" in refinement, chi squareds traffic lights, sequence assignment, improved key-bindings, improved NCS tools, integration of Molprobity rotamer probabilities, the move to PDB 3.x format compliance, and a restraints editor. It is already the de-facto standard in model building. Stuart McNicholas as per agreement from WG1 is now leading the development of CCP4MG. Not only is the QT (more robust code) version more stable and faster but the graphics are extremely good. The latest version has the COOT button which allows seamless transfer between the programs. The latest stable release is part of CCP4 but can also be loaded from the MG site. The QT version will be released this month (Jan 09).
(6.2) MOSFLM (and its GUI). We fund one person to work with Harry Powell (who is grant funded). Both gui and MOSFLM continue to improve significantly. The new spot finding algorithm is much more powerful. Full TESTGEN functionality has now been incorporated, plus the facility to process images as they are being collected. Almost all the functionality of ipmosflm is now available. The GUI creates a new standard in usability and reduces button pressing to a minimum, e.g. it is now possible to press one button to index, select spacegroup and calculate mosaic spread. It is now being rolled out across synchrotrons and I urge people to upload it. In the near future it will become possible to test space groups (pointless) and scale data during image integration. Corrections to handle detector corners (important in 3 x 3 detectors) in AIMLESS are being developed in collaboration between MOSFLM team and Phil Evans.
(6.3) PIMS: We currently fund two positions. The Executive will schedule and conduct (with outside help) a review of continued CCP4 support (akin to that for the MG initiative). Unlike MG, we are not the only stakeholder, thus we cannot "direct" the project entirely.
PiMS is now used by MPSI, SSPF, and the OPPF in the UK, and also IRB, ISB, and CSIRO. We are in discussion with three companies about commercial licences for PiMS. PiMS will remain free for academic use. The licences are based on the CCP4 licences.
PiMS2.2 is product grade, with a range of features covering most aspects of protein production. The benefits it provides include traceability, searchability, manageability, continuity, flexibility, and future proofing. Planned work includes completion of xtalPiMS, integration with synchrotron facilities, a hosted service, usability improvements, better construct management, better scaling for large labs, and instrument integration.
We envisage that the future of PiMS is under the INSTRUCT umbrella, and are seeking bridging funding to cover FY2010. We hope to show that PiMS the right vehicle for the BBSRC's goal of sharing experimental data, in the case of protein production. www.pims.ac.uk
(6.4) Molecular replacement: We support MrBUMP and Balbes and benefit enormously from PHASER. Plans to upgrade MrBUMP to deal with protein-protein complexes are imminent. We will explore a possible web service for this.
(6.5) Experimental phasing and model improvement: We are going to make a push to implement automated front ends (in some ways analogous to MrBUMP) to utilise the powerful software we have developed. The programs PARROT and BUCANEER (Kevin Cowtan et al,) will be
introduced in version 6.1. PARROT is a new density modification program to replace DM – it is
fully automated (requiring just sequence and MTZ, and optionally heavy atoms or model for NCS),
and gives substantially better results than DM without taking significantly longer to run. BUCCANEER continues to evolve; it is fast, robust and competitive over a range of resolutions, and provides best-of-class results for low resolution problems (2.8-3.6A). The version of PHASER released with 6.1 gives us new tools to calculate phases from SAD information, starting from a substructure or even a molecular replacement model.
(6.6) Refinement: The new REFMAC with refinement of twinned data is now available. Its performance suggests this is the best in the class. The procedure is fully automatic once the twin is selected and the new GUI makes this very easy. SAD refinement is close to completion. We are aware that there remain issues with low resolution for the most challenging projects. Escaping from the tyranny of anecdotes by properly evaluating performance is underway and we expect further improvements. There has been an overhaul of dictionaries, the funding of PRODRG and JLIGAND will mean more easy-to-use and robust libraries for refinement.
(6.7) New GUI: We fund Liz Potterton and she will fill the role of scoping out and designing the new GUI. There will be a series of meetings to establish what users want, how it can be delivered and on what time scale. It seems likely that we will use QT as the graphical toolkit.
(6.8) The core suite: This remains our biggest investment. The current team have worked heroically to release 6.1. We all recognise that the way we manage releases has to change, the suite has grown too large and too complex to continue to work as before. One serious problem has been fixing broken code (which might not compile on some platforms), assuming delivery of fixes and rewriting GUI’s. The multiple UNIX flavours have complicated this task. New testing procedures, common program repositories and automatic nightly building are planned to lead to a more rapid release schedule. The precise model for future releases remains unclear and is being scoped out. It is a high priority to make this automatic and seamless. We are committed to an overhaul of the PDB format (when changed by the PDB) and an extension to the mtz format within the next few years.
We ask that WG1 agree to de-emphasize (with a view to discontinuing) IRIX support.
We may also come forward with proposals next year to focus on fewer LINUX flavours. Any such suggestions would be based on extensive consultation with the user community.
CCP4 will continue to support workshops, both within the UK PX community and worldwide.
The Summer School was organised and run by Elspeth Garman and Martin Noble. It was a resounding success, and we send Elspeth and Martin our congratulations and thanks.
Garry Taylor and Jim Naismith will run the summer school in 2009.
Expenditure on outreach activities
South West Structural Biology ?8k
Oxford summer school ?9k
Carlisle (Northern) ?7.25k
8 Licence issues
9 Research Complex at RAL
In September Ronan Keegan and Charles Ballard will move to RAL into the Research Complex at Harwell (RCaH), which will be completed at the end of September 2009. The terms of this move have been agreed. Normal Stein will leave CCP4 around this time, having declined to move. We will advertise two new positions in the New Year to be filled at RCaH at around the September time frame. Martyn will continue to be part time (decreasing percentage) while he remains in Daresbury.
10 Other matters
The Executive will ask that a second CCP4 fellowship is created (Paul Emsley currently holds the original one). The Executive (minus Kevin Cowtan) has been in discussion with York University on issues surrounding Kevin’s future involvement with CCP4 and his position at York. It seems likely
that an arrangement where Kevin is offered a deferred CCP4 fellowship in 2009 to be taken up at the end of a grant (2013) will result in York giving Kevin a fully underwritten independent permanent academic position. York will agree to accept the risk that CCP4 may become insolvent between now and 2013 (or at any time thereafter). CCP4 would agree that the fellowship offer will be made in 2013, provided funds are available. Long term or large commitments require WG1 approval since in this case we propose agreeing to funding almost 10 years in the future, it must be a community decision. The Executive (minus Kevin) strongly support this proposition and recommend WG1 adopt it. The Executive feels there is a window of opportunity at present. The Chair is happy to discuss the matter with any member of WG1.
Kevin's contributions to CCP4 over the years have been substantial, including:
; Core libraries: the Clipper libraries provide the basis for COOT, CCP4MG, PARROT and
BUCCANEER, and are also used in CTRUNCATE, POINTLESS, AIMLESS, ARP/wARP
and a number of other projects worldwide.
; Major applications: DM, DMMULTI, FFFEAR, PROFESSS, PARROT, BUCCANEER
; Minor applications: MAPMASK, NCSMASK, CFFT, CINVFFT, CSFCALC,
CPATTERSON, CHLTOFOM, CSIGMAA, CPHASECOMBINE, CPHASEMATCH,
CANISO, CECALC, CSEQUINS, CSYMMATCH, CONVERT2MTZ
; Program output: Initial author of JLogGraph inline graph viewer, contributor to the
BAUBLES program output annotation tool.
; Documentation: Creator of and principal contributor to the ccp4wiki.org documentation
; Teaching and outreach: Outstanding regular tutor at CCP4 and other workshops, teaching a
range of CCP4 software.
; Funding: Major contributor to the 2008 CCP4 grant renewal.
CCP4 Working Party reports Nov 2008
WORKING PARTY 0: Core activities
COORDINATOR: Keith Wilson (KW)
Martyn Winn (MDW), Peter Briggs (PB), Charles Ballard (CB), Francois Remacle (FR), Ronan Keegan (RK) and Norman Stein (NS)
MARCH - NOVEMBER 2008
; Releases How much achieved:
; Get 6.1 our asap. To be the last monolithic release. CLOSE.
; Step back and decide exactly what we want. (whole team). TO BE DONE.
; Aim for package releases. Establish system for automated release of individual modules as
they are updated. Coordinate with developers. (core team + developers) 6-monthly
announcement of latest contents. How to identify set of versions in a given snapshot. Action:
Plan what the packages are, especially what goes into the core packages. (MW to lead).
; Survey other software projects of comparable size (MW) NOT DONE.
; Automatically inform users when new versions are available. (FR) FR LEFT.
; Coordinate between packages which have inter-dependencies.
; Regression testing: a workshop to initiate this? NOT DONE.
; Developers to establish appropriate test data to simplify full testing on platforms by the core
team and effectively devolve some this onerous tasks from the core to the developers. (PE
proposal) IN HAND. GW has started acquiring data
; AA requested email list for system admins, tools for addressing a multi-user shared
environment, and an approach to exploiting big computers (and multi-core desktops) NOT
; Core staff:
o Recruit replacements for Peter and Maeri asap. These posts should be based at Rutherford,
but conflict with continuity of experience and induction to the team. DELAY OF MOVE
o Peter replacement to work on the GUI/database with Liz as required by the grant. Should
have this person in place in October. FR first choice, but left CCP4. This is on hold till
o Recruit MH replacement to lower finance and admin load on Charles. Spending much too
much time on finance details at present. OCT 09 IN RUTHERFORD
o Continue to monitor times on the various areas over a longer period (MW to coordinate).
o Revisit Martyn’s questions about whether some aspects of support can be dropped. This
may be helped by the Wiki developments. IN PROGRESS
; Research activities of core team:
o Vital that core team have some time to devote to research and development.
o Need to be flexible wrt to the projects on which research staff are focused, not just continue
with the status quo. Need a consensus with core team
o Review areas of research for the team. (KSW) NOT DONE GIVEN LOSS OF STAFF
; Relocation: DELAYED UNTIL OCT 2009
o Research complex to house CCP4 at Rutherford. Completion date late 2009.
o CBB and RK to relocate Sept/Oct 2009.
o PB and FR resigned. NS elected not to move, but appointed 1 more year.
WORKING PARTY 1: Program output, Manual & WIKI, Publicity Material
COORDINATOR: Martyn Winn (MDW)
Kevin Cowtan (KC), Phil Evans (PRE), Eleanor Dodson (EJD), Graeme Winter (GW)
ACTIVITIES April 08 TO PRESENT
o MDW has taken over as coordinator of WP1
; Baubles/Program Output:
o PJB has documented Baubles at http://www.ccp4.ac.uk/group/documents/pjb_projects.php
o Baubles incorporated into main CCP4 and included in CCP4i for test releases 6.0.99a
onwards (ccp4i: “View Annotated Log in Web Browser”)
o Baubelised programs: buccaneer, parrot, scala, pointless, phaser (latest version, not in
o GW polled ccp4-dev on programs to update (1 response)
o FR wrote new Java version "JLogView" which can run as standalone application or as
o Finished but not yet in test release series.
o FR drew up a draft new loggraph markup specification (new_markup.doc). Available on
internal pages - not sure if circulated.
o Up and running
o KC has provided regular summaries of contributions.
o Looked at by MDW. Summary to be presented in Nov 08 talk.