\documentstyle[a4,11pt]{article} \headheight 0mm % No header text \headsep 0mm % No distance between header and body of text %\parindent 0mm % No paragraph indentation %\parskip 5mm % Size of gap between paragraphs \addtolength{\textheight}{.2in} \textwidth 14.5cm \oddsidemargin 0.0cm \evensidemargin 0.0cm \begingroup\makeatletter \def\section{\@startsection{section}{1} {\z@}{-2.5ex plus -0.5ex minus -0.1ex}{0.5ex plus 0.1ex}{\reset@font\bf}} \endgroup \begin{document} \begin{center} \large\bf MINUTES OF THE WORKING GROUP 2 MEETING OF CCP4 HELD AT YORK ON 7th JUNE 1995 \end{center}\vspace{5ex} \noindent{\it Present:} \noindent \begin{tabular}{@{}l@{\hspace*{2em}}l} \\ David Rice (Chairman) & Sheffield University \\ Phil Evans & MRC, Cambridge \\ Adam Ralph (Acting Secretary) & Daresbury Laboratory \\ Don Akrigg & Leeds University \\ Peter Daly & ESRF Grenoble \\ Eleanor Dodson & York University \\ Madeline Moore & York University \\ Cameron Dunn & Bristol University \\ %Paul Emsley & Glasgow University \\ %Neil Isaacs & Glasgow University \\ Sheila Gover & Oxford University \\ %Paul Holden & Bristol University \\ Peter Keller & Bath University \\ %David Love & Daresbury Laboratory \\ %Adam Ralph & Daresbury Laboratory \\ %Sandra McLaughlin & Hamburg \\ %Simon Phillips & Leeds University \\ Jim Raftery & Manchester University \\ %Ian Tickle & Birkbeck College \\ %Jan Zelinka & York University \\ Kevin Cowtan & York University \\ David Waller & Sheffield University \\ Garib Murshuolov & York University \\ Tadeusz Skarzynski (Industrial rep) & Glaxo \\ %Steve Yewdall & Edinburgh University \\ %Ian Clifton & Oxford University \\ Paul Hempstead & Sheffield University \\ Misha Isupov & Exeter University \\ Peter Brick & Imperial College \end{tabular}\vspace{2ex} \noindent{\it Apologies: } Neil Isaacs, Ian Tickle, Dave Love, Paul Holden, Simon Phillips. \section{Minutes of the previous meeting and matters arising} The minutes of the meeting held on 1st March were agreed without corrections. On matters arising David Rice asked about what had been done with respect to Michael Rossman's programs. Kevin Cowtan said that when DM was tested on a virus (c. 320 Angstroms cell edge) it used alot of memory and was slow. However, there were other programs available for viriuses written by Fred Vellieux (DEMON) and Jan-Pieter Abrahams (SOLOMON). \section{ Study Weekend 96} Eleanor Dodson described a rough outline of the program (see separate sheet). After the FreeR workshop (see section 4) she felt that some of the same people from the workshop should be invited to talk. People felt that there still needed to be some more thought about the overall structure of the meeting. It was suggested that modelling of disorder should be included, possible speakers were Pete Gross, Miroslav Papiz or George Sheldrick. Other topics mentioned were refinement with pseudo-symmetry (talk by small molecule or DNA crystallographer), partial structure refinement, free sigmaa (Randy Read) and possibly a talk by Gerard K. about using NMR structures as MR models. Generally it was decided that less emphasis should be placed on high resolution structures and more on intermediate and low ones. Also, that the speakers should be advised that they should present their talks in such a way as to cater for inexperienced crystallographers. There was a general call from Eleanor for people to suggest speakers particularly people that were having or had problems with refinement. Action: Eleanor, Madeline \section{Finances} It was pointed out that the estimated under spend this financial year would be bigger than last, in the region of 100K. Although the extra staff member was not taken into account (see section 5) neither was the increase in the industrial user base. This seems to be increasing particularly in America and Japan. With this in mind it was decided to fund the Northern Crystallographers Workshop to the tune of \pounds2000. However, it was suggested that the name of the workshop should be changed to include 'CCP4'. It was also agreed that other such workshops could be funded, even though they were geographically limited in order to keep the numbers small. All funding of these events need the aproval of the committee. Action: Adam \section{FreeR workshop held at York} About 40 people attended this workshop. Eleanor believed that it was a success and that it stimulated valuable dicussions. As the EU funding was more than generous there was little call on CCP4 funds. The program is given on a separate sheet and the workshop report will appear in the next CCP4 newsletter. \section{Investment in hardware/personnel } A new temporary post will be advertised externally on 22nd June. The remit will be similar to Adam Ralph's and the contract will be a two year one. This new person will require a terminal and it was suggested that the maximum amount spent on this should be 7.5K. A new disk has been purchased for the anonymous ftp area. The old one was flakey and needed replacing. However, it was also pointed out that data transfer was very slow from abroad, particularly America. It was suggested that a mirror site should be set up in America, probably at Brookhaven. Dave Love pointed out (after the meeting) that in order to do this we would need to alter the distribution conditions. Thus this would need to be ratified by WG1. We would like to wellcome Peter Keller as a new member of CCP4. He has a six month contract to look into mmCIF and write some routines to read and write it. Action Dave, Adam, WG1 \section{mmCIF} mmCIF will be formally announced at the next ACA meeting in Canada. Currently there are three programs in the public domain that will read/write CIF: STARBASE, ZINC, CIFTBF. However, because of the constant changes in the format of mmCIF only STARBASE can interact with the current definition of mmCIF. Peter Keller's remit is to write routines that will read/write coordinate files in CIF format. These routines will not replace the RWBROOK subroutines, thus it should be possible to read/write either PDB or CIF files. CIF is based on STAR format which Peter feels is floored because it does not take into account different machine/file attributes. It was pointed out that we could just have a PDBtoCIF and CIFtoPDB programs. However, this might be difficult and as Peter says he is not trying to justify mmCIF only to make sure we have the option of using it. Peter will be attending the ACA meeting and will give us a report at the next WG2 meeting. Action: Peter \section{Boisym Meeting} Cameron Dunn attended the meeting and described the Biosym package as it stands at the moment. It is based on Insight at the top level. Under this is Xsight which calls groups of programs (modules). Although not as complete as CCP4 you can go from solving your Patterson to building the structure in one contained package using a GUI. Cameron said he was impressed with Duncan McRee's Xtalview which was very quick at solving Pattersons. The demo they had on show took 10 minutes to solve a structure. However, the standalone version of Xtalview was faster than the version used by Biosym. Phil pointed out that you can get Xtalview free at the moment! However, it unlikely to be the same version used with the Biosym package. However, Xtalview was funded by the US government and thus will be developed and free to academics. It is ported to HP, SUN, DEC Alpha (OSF1 and PHIGS) and Linux. Also, included with the package is PROLSQ which has an automatic PROTIN step e.g. looks for NCS and secondary structure. It also has Monte Carlo conformational searchs for loops and interfaces with a dynamics package (DISCOVER). The MR module was basic but did have a dubiously helpful 3D display of the results. There is also a PROCHECK like program which highlights outliers graphically. Cameron also said that they had a help service which would be viewed by a panel of people and not the whole world. Adam pointed out that this already existed within CCP4 by the fact that you can send mail to ccp4@dl. The cost of the suite to academics appears to be 5K per site (1 server and 3 processors) for sites with Insight. However, Insight costs 2-3K per processor plus high performance graphics is needed. The general feeling was that CCP4 would still be favoured by academics as it is effectively free to them. Of course the biggest worry would be if we lost the industrial users. Tadeusz Skarzynski said that although the Biosym package had some good points, it was not complete and it would cost much more to them than the above figures. Biosym will be giving a demostration at the ACA meeting and by then they hope that they would have filled in some of the gaps e.g. DM techniques. \section{A New Refinement Program} Garib Murshuolov gave an interesting talk about the new refinement program he is developing. Its main feature is that it uses maximum likelihood techniques which make it possible to take into account phase errors and prior phase distributions. Garib says that the program is almost ready and that he is willing to let people test it. \section{FAQ and MR tutorial} Paul Hempstead has produced a first draft of the FAQ which contains Dave Love's original plus questions and answers from CCP4bb. A couple of points were made about the FAQ in that answers should be addressed in a general manner and not contain references to the questioners. Also, that the general section should be split into two parts at least e.g. machine specific problems and data/file format errors. For maintaining the FAQ questions and answers would need to goto Paul. Unfortunately, it is not possible to do this automatically from the bulletin board itself. It was suggested that people should be encouraged to send a summary of the answers they receive to the bulletin board. The MR tutorial is now completed and has been sent to Sue Bailey. Action: Paul,Adam \section{DM} DMmulti has been released, this covers multi-crystal averaging. The program was released quickly before the CCP4 funding ran out. Therefore, it would be useful if the community reported any problems. The phase combination part of DM is being rewritten and hopefully this will enable Jan Pieter Abraham's density flipping to be included. There are still some holes in the suite with respect density modifaction. Finding a mask using correlation maps cannot be done in DM but can in DEMON. DEMON is being modified by ther authour Fred Vellieux to be consistant with CCP4 programs. Also, map modifactions ala MAVE/RAVE are not possible in CCP4. Kevin plans to write a new program (MAPROT?) which will cover these options. SOLOMON written by Jan Pieter was also considered to be a useful addition to the Suite. However, at the moment it is rather machine specific. Action: Kevin \section{Programs} \begin{enumerate} \item{} Renaming of all routines, to eliminate name clashes, was considered too traumatic. However, it was agreed that specific clashes may have to be resolved. \item{} Zldb: Jan Z. said that he was not interested in extracting the graphics routines from Zldb, although he may give us the code. There was some discussion about whether GL would become a graphical standard and the fact that these graphics programs cannot be used on Xterms. (See PLUTO) \item{} Almn: Should be kept. \item{} PLUTO: It was agreed that PLUTO should be removed. However, Dave Waller said that Ito had written a program SkullD which could be used to replace or compliment NPO. Action: Dave Waller \item{} Prmap, Envelope, Reslice: It was agreed that these programs should become unsupported. \end{enumerate} \section{Any other business} It was decided that the membership of the committee should extend to take in one person from each group plus program developers. However, if the meetings were to become too large, steps may need to be taken to reduce its size. Action: Adam \\ Adam Ralph indicated that there maybe interest in a workshop specifically focused on using CCP4 programs. It was suggested that an e-mail should be sent to the bulletin board asking how many people would like such a workshop. Action: Adam \\ MOSFLM was being changed to eliminate the need for the 'with-mosflm' compiler option. Phil Evans suggested that PARSER might be changed to include a backslash as a line continuation. Action: Adam \\ Kevin Cowtan said he would change AMORE so that it could do MR on maps without reference to the data. Action: Kevin \\ The current version of PROCHECK has some problems in the current distrbution. Adam Ralph was not sure why some of the problems occured but would look into it. Don Akrigg said that Roman was keen to make the program more portable. One way of doing this would be to use the CCP4 libraries. Adam said he had contacted Roman Lakowski on this matter but had not had a response. Eleanor Dodson said that the suite was being changed so that unobserved reflections would be included in the MTZ file but be flagged with a magic number. This work is in progress. Finally, Phil Evans said that Keith Wilson had set up an EU network on 'Methods in Macromolecular Crystallography'. This would enable people working on method developement to travel and work at a foreign node. If interested contact Phil Evans or Keith Wilson. \section{Venue and date of the next meeting} The next meeting was set for Wednesday, 6th September 1995 at Birkbeck College at \mbox{11--30~am}. \vspace{2ex} \end{document}