\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}{.5in} \textwidth 14.0cm \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 BIRKBECK COLLEGE ON 30th SEPTEMBER 1993 \end{center}\vspace{5ex} \noindent{\it Present:} \noindent \begin{tabular}{@{}l@{\hspace*{2em}}l} \\ Phil Evans (acting Chairman) & MRC, Cambridge \\ Sue Bailey (Secretary) & Daresbury Laboratory \\ Don Akrigg & Leeds University \\ Peter Daly & ESRF Grenoble \\ Eleanor Dodson & York University \\ Cameron Dunn & Bristol University \\ %Paul Emsley & Glasgow University \\ Sheila Gover & Oxford University \\ Paul Holden & Bristol University \\ %Rod Hubbard & York University \\ Peter Keller & Bath University \\ David Love & Daresbury Laboratory \\ %Sandra McLaughlin & Hamburg \\ %Simon Phillips & Leeds University \\ Jim Raftery & Manchester University \\ %Lindsay Sawyer & Edinburgh University \\ Ian Tickle & Birkbeck College \\ Jan Zelinka & York University \\ Dave Waller & Leeds University \\ %Garib Murshuolov & York University \\ Alan Wonacott (Industrial rep) & Glaxo \\ Steve Yewdall & Edinburgh University \\ \end{tabular}\vspace{2ex} \noindent{\it Apologies:\/} David Rice, Simon Phillips, Sandra McLaughlin, Wojtek Rypniewski. \section{Minutes of the previous meeting and matters arising} The minutes of the meeting held on June 16th, 1993 were agreed. \section{Talks with Alwyn} Phil, Eleanor and Jan had discussions with Alwyn Jones while he was visiting York. O, RAVE and other software from Alwyn's group are available by ftp from Uppsala as executables. They use CCP4 libraries and integrate with CCP4 programs, but Alwyn does not want them to be a part of CCP4. Alan Wonacott asked about the implications for industrial users and Phil confirmed that Alwyn was hoping to raise some money to help pay Gerard Kleywegt by selling programs to companies. Phil was not very happy about people only distributing executable code as this could cause problems on some machines, however, so long as someone was actively updating the programs he did not think this was a problem. Fragmentation of software, needing to collect different programs from various sources is a nuisance and is the reason CCP4 was set up. It was pointed out that CCP4 did not have an averaging program and could only point people towards using RAVE. For completeness CCP4 ought to include this capability (especially for distribution to commercial users). Sheila agreed to ask Jonathan Grimes about including his program and Ian T.\ said that he had also written a program which was now space group general but which did not deal with improper symmetry. The secretary asked if skewplanes could be withdrawn from distribution and this was agreed.\\ ACTION Sheila \section{Commercial Software} Communications have been received from Charles Collyer at Pharmitalia and Nigel Walker at BASF saying they are unhappy with the current arrangements for the distribution of CCP4 to industrial companies. They think \pounds5000 is too much to pay each year. Alan also summarised the views of several other companies that he had been in touch with. The secretary suggested sending a letter to all companies using CCP4 to see what they thought reasonable arrangements would be. It was agreed that this should be done in collaboration with Alan. The results of this survey could then be used to formulate a new policy if necessary. The chairman was pleased to see Alan on the committee as a representative of the industrial users. \\ ACTION Sue \section{Finance} The secretary informed the group that CCP4 had received \pounds50,000 from industrial users so far this financial year. This was more than enough to subsidise the January meeting. There was some discussion of ways to prevent the money being lost at year end. The intention was to ask David Rice to look into setting up a University account, into which some of this money could be transferred, to enable CCP4 to carry the money over from one year to the next. \\ ACTION Dave Rice, Sue David L. suggested spending some of the money on a replacement for the $\mu$VAX at Daresbury, as the machine was very slow and wasted his time. Dave uses the Vax for writing tapes and for development work. Access to a VMS machine is essential for testing compilation and running of the programs under VMS. A possible replacement might be an Alpha running under VMS. Dave Waller pointed out that groups with Alpha/VMS were struggling. It was agreed that Daresbury needs VMS capability and Dave should find out how much a suitable machine with peripherals would cost and report back to the next WG2 meeting. \\ ACTION Dave Love \section{Status of '93 Study weekend proceedings} The secretary reported that these have been compiled and are with the printing section at DL\@. It is hoped that they will be distributed within the next few weeks. \section{1994 Study Weekend} Dave Waller distributed a list of invited speakers (all accepted except one yet to confirm) and possible case studies. The number of talks was to be restricted to 15--16 as agreed at previous meetings. Eleanor wanted to know how these talks would be divided into sessions and what the topics of the sessions would be. It was generally felt to be important to decide this in advance of writing to speakers so that the speakers can be told what topics they should cover. The chairman for the final discussion session was discussed and it was felt that Alwyn would be very good especially if he had the last talk and the discussion could follow on from this. Other possible case studies were asked for and several names were suggested. Announcements of the meeting were being prepared at DL and should be sent out the following week. The closing date for applications is 19th November and the intention is to be very strict and not allow late applications. Members of the WG were asked to point this out to members of their laboratories to avoid disappointments. \section{Documentation Workshop} The secretary thanked the people who had attended the documentation workshop, held in York on 13th-16th September. A lot of documentation had been looked at and hopefully improved. Dave L.\ responded that he had not yet retrieved and integrated the updated documentation as it was still being changed. It was agreed that all work on this area would cease so that Dave could ftp everything back to DL and start incorporating the documentation into the new version of the suite. Eleanor asked that people read the updated documentation and report any problems or areas that are difficult to understand so that the documentation could be further improved. \section{Standard Image Formats} Peter Daly reported that version 1.0 of the routines for handling standard image formats is completed and will be available by ftp in the near future. There are libraries and documentation available. Peter agreed to send a message to CCP4BB as soon as the ftp area was set up. Phil thought that we should make all the processing programs able to use this standard format. A conversion program or programs are needed to convert all existing formats to the standard. Peter said that a conversion program already existed. Peter wanted to keep the distribution to executable modules to avoid divergence of the source code. Phil felt it was important to distribute source code as well as changes need to be made for some machines. Peter also agreed to distribute the current keywords, available for protein crystallography, for comments. Ian Tickle asked if the routines used FREAD and FWRITE (they do) as these are very slow on a VAX. \\ ACTION Peter Daly. \section{CIF Format} Eleanor and Jan are to attend a meeting on the macromolecular CIF format. Eleanor said that there is already an interactive program available for converting from PDB to CIF format. There is a lot of extra information in the CIF format and the program asks the user questions to get this information. The extra information will be an advantage to people analysing structures on the graphics but is not very useful for protein crystallographers. However there are currently no tools for using this information or for creating it. Garib Murshudov at York is writing a library of routines for reading and writing CIF files. These will be called instead of RWBROOK routines and will extract the same information. Protin will need quite a few changes but other programs should just need the subroutine calls replacing. \section{State of Programs} \begin{enumerate} \item{} Version 2.2. Dave Love said this should be ready by the end of October. Dave had come across some problems implementing the changes to create portable binary files in a general way, but this was now all done. Assembler library routines, used on VMS machines, had been removed and replaced with C-routines. Dave pointed out that files written by the assembler routines cannot be read by the C-routines and will need to be converted with a separate program, but Peter Keller described a way of getting round this problem without having to convert files. Many changes had been made to the documentation at the workshop and these still had to be integrated into the distributed version of the suite. Once this was done Dave will announce the new version on CCP4BB. Ian Tickle has rewritten some of the C-library routines in FORTRAN. It was agreed that these should not be included in version 2.2 as they would delay its release. Eleanor thought some labs should be using the library code for portable file formats to test it out before release. Programs added for the new version are: ACT, AMORE, GENSYM, NPO, PROCHECK, UNDUPL, RSPS and VOLUME. Some programs have been removed from the suite and are no longer distributed. Don thought that we should discuss which programs are to be supported and unsupported. It was agreed to do this at the next WG2 meeting. Dave Love said that in future he did not intend to fully optimise code for running on SG's as there were bugs in each version of the SG optimiser which has caused programs to crash. ACTION: Dave Love \item{}Magic numbers. Eleanor reminded us of the intention to use `magic numbers' in the MTZ files to signal absent data. There was some discussion of the best way of doing this. One way is to use NaNs (Not A Number) on archictures that support the concept. Dave Love had already implemented two new routines in consultation with Phil: QNAN --- a function which returns a `magic number' appropriate for the architecture, e.g.\ a NaN; and QISNAN --- a function to test if its argument is a `magic' value (takes argument and returns logical). Using magic numbers will involve a lot of work as so many programs will need changing. \item{} Running under Alpha/VMS. There is a problem with FSEEK on Alpha/VMS machines and Dave Love has made changes to library routines to get round this. Dave Love agreed to give Leeds the modified library to test. Dave Waller reported that this did not seem to be the only problem on Alpha/VMS systems, he had found another problem in SFALL. \\ ACTION Dave Love, Don Akrigg and Dave Waller. \item{} Xloggraph. Jan reported that problems with Xloggraph on SG's running v.5 operating system had been corrected and Dave Love had got it working under SunOS. \item{} Amore size problems. CCP4 has received complaints from users unable to link or run Amore because it uses too much space. Eleanor said that Amore was written for IBM machines and did all FFT's in real memory which required a lot of space. The space needed by the program was discussed---if arrays in the program are dimensioned for a large protein, many people will be unable to link the program. Changing the size of the arrays is not trivial due to the complicated way in which data is handled internally. It was agreed that Dave Love should obtain a smaller version of the program from Eleanor for future distribution. Warnings are already included in the documentation about the program needing a lot of space. One possible long term option is to replace the FFT routines with ccp4 routines, but then this would slow the program down. \\ ACTION Dave Love, Eleanor. \end{enumerate} \section{Any other business} Phil announced a new program Scala which he has written to replace Rotavata. He asked people to test the program and give him some feedback. The program can be used in Rotavata mode to calculate batch scale and temperature factors or a number of parameters can be adjusted to give scale factors which vary depending on the way the parameters are set (following methods by Kabsch). Phil warned that the program can be very slow to run if a number of parameters are used. When writing the program Phil had used the INCLUDE option for common blocks etc. and he wondered if this was a better way of storing programs: each program in a separate directory, rather than a single file for each program. Dave Love said that for distribution he preferred not to have each program in its own directory with include files but would look into build procedures to cope with this. Phil said that Jan Pieter Abrahams was writing a C-interface for reading MTZ files, which uses the FORTRAN routines. \section{Venue and date of the next meeting} The next meeting was set for Tuesday, December 14th 1993 at York, Chemistry Department \mbox{11--30~am}.\vspace{2ex} \noindent ---Sue Bailey (secretary) \end{document}