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CCP4 Refinement Workshop

Monday 1st September to Friday 5th September, University of York

Organisers: Eleanor Dodson (York) and Jim Naismith (St. Andrews)


Working Group 1 decided that CCP4 should try to promote best practice amongst young crystallographers. The rationale being that the development in software has been so rapid that most labs do not have in-house expertise in all the major programs. It was thought that refinement techniques would be a useful starting point for such a course. Eleanor and Jim agreed to organise such a course in York.

Format of the course

We decided to split the course into tutorials and lectures. Initially we planned to accept only 20 students but we ended with 27 actually doing the tutorials. This is roughly one person per UK crystallography laboratory. The lectures were open to all and advertised via the CCP4 Bulletin Board. We actually rejected over 30 applicants. Amongst those were several from the USA. (Eleanor and Jim hereby volunteer to organise a repeat meeting in Florida preferably in February!) The timetable that was actually followed can be seen by clicking here. Some lecturers have already supplied Web formatted notes, others have promised and Jim is typing up his notes of the others. A full set of notes is planned to be available on the Web soon (see the program for details) and certainly by the end of November. An announcement will be made on the CCP4 Bulletin Board

Highlights of the course

The lecturers were all superb. David Watkin started the students off with an insight into what refinement actually means and what we actually do. Eleanor reminded us how to collect data. The importance of getting our structures right was underlined with a superb talk by Guy Dodson, who spoke about the buckling of the heme ring in hemoglobin and its biological implications. It would be fair to say Dale Tronrud stole the workshop, he combined powerful insight with a sense of humour. He got down in the F's and xyz's with the students and all professed to expert TNT users by the end. Paul Adams gave us a preview of CNS and gave a good explanation of torsional dynamics, again Paul helped the students run their scripts and iron out problems. Randy Read and Raj Pannu discussed maximum likelihood and its implementation in many software packages. Randy showed convincing evidence of the power of this technique. Both Raj and Randy helped out the CNS strugglers. Garib Murshadov told us how to run REFMAC and advertised improvements to come. Both he and Eleanor spent an afternoon and evening getting students using REFMAC like experts. Ian Tickle's presentation on RESTRAIN exposed the students to the concepts of TLS which is currently only implemented in RESTRAIN, Ian also helped students run these jobs. Isabel Unson gave a very good overview of SHELXPRO and got those with high resolution data started on this software. The theme of accuracy, precision and validation lead by Durward Cruikshank, Tom Oldfield and David Moss stimulated some of the most thought provoking discussion with Eleanor Dodson, Isabel Unson, Dale Tronrud, Jim Naismith, Ian Tickle and Randy Read all contributing to the argument. Tom Oldfield and Kevin Cowtan spoke about maps and their ideas and hints were of use to everyone, Zbigniew Dauter told us how to put in waters quickly and accurately. Kim Hendrick from EBI emphasised that if our results are to mean anything they have to be accessible to biologists. He talked about the new developments at EBI. Jim Naismith tried to explain the idiosyncrasies of the PDB, initiated the students into the mmCIF society and preached submission. Alexei Vegan and Richard Greaves wound up the meeting by outlining how to build dictionaries for those new ligands. Eleanor and Guy hosted a party on Friday evening/ Saturday morning where the students handed out presents to thank the speakers and organisers. Thoroughly the worse for wear we all departed Saturday morning.

Problems of the course

The principal complaint of the students that 27 was too many for the tutorials. This is probably true but choosing between people from different Universities was invidious and some people made late but compelling cases for inclusion. In the end we felt it better to have 27 people 80% satisfied rather than 20 people 90% satisfied.


Jim and Eleanor are enormously grateful to all those who spoke and demonstrated, without them there would have been no course. The staff at York were very helpful and made sure things went smoother than they should have done. The students were fantastic and did not complain when the organisation went off the rails. No UK student/post-doc had to pay a penny to come thanks to CCP4.

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