\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 BIRKBECK COLLEGE ON 28th SEPTEMBER 1994 \end{center}\vspace{5ex} \noindent{\it Present:} \noindent \begin{tabular}{@{}l@{\hspace*{2em}}l} \\ David Rice (Chairman) & Sheffield University \\ Phil Evans & 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 \\ 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 \\ %Lindsay Sawyer & Edinburgh University \\ Ian Tickle & Birkbeck College \\ Jan Zelinka & York University \\ Kevin Cowtan & York University \\ %David Waller & Leeds University \\ %Garib Murshuolov & York University \\ %Alan Wonacott (Industrial rep) & Glaxo \\ %Steve Yewdall & Edinburgh University \\ %Ian Clifton & Oxford University \end{tabular}\vspace{2ex} \noindent{\it Apologies: } Lindsay Sawyer, Steve Yewdall, Paul Emsley, Simon Phillips, Bill Hunter \section{Minutes of the previous meeting and matters arising} The chairman apologised for missing the last two meetings and after introductions new members of staff were welcomed. The minutes of the meeting held on 28th June were agreed. The chairman noted that matters arising from the minutes were on the agenda already. \section{ Study Weekend} The secretary handed round copies of the meeting programme and explained that all speakers had agreed to come. It was suggested that the organisers make a programme deciding the subject matter for each of the speakers and then communicate this to the speakers, stressing the need to keep to their allocated subject in order to minimise overlap between talks. The working group went through the list of speakers giving some ideas of the directions the speakers should (and should not) take. These ideas were forwarded to the meeting organisers. The secretary confirmed that Chester College had been booked for Friday 6/Saturday 7 January and that the Daresbury conference office had started work on arrangements \\ ACTION: Janet, Bill, Sue \section{Finance} Sue drew attention to the large positive income. The income for the present financial year assumes all companies promising to renew each year do so (they have so far). There was some discussion on what to spend the money on or whether we should reduce the price of the programs. There was support for keeping the price as it is and using the money to invest in the software. Other suggestions were support for a Como meeting to be held next year and running workshops, for industrial and academic users covering how to run and use the programs. The secretary supported the idea of workshops although she wondered if there was conflict with the Bath Summer school. Priorities for spending were agreed: 1. Extra personnel to improve the programs, 2. Support for study weekend. 3. Support for other meetings. Phil identified two types of improvements for the suite: development of basic ideas and packaging of the suite. Both were felt to be important, although the development work involves having an appropriate person to do the work. Kevin asked whether we want to diversify into graphics, as solving a structure can now involve use of graphics at earlier stages, eg for Prism type programs. David R. noted that we have previously decided not to copy programs already available. However it was recognised that we no longer have the same access to programs written by others. \section{Biosym and Oxford Molecular}- Please keep confidential Neil updated the working group on communications with Biosym. A letter had been sent to Biosym, giving the points CCP4 had made at the last WG meeting. The response from Biosym agreed to some conditions but not others. Sue felt that this response was not very positive for CCP4 and replied asking Biosym to explain any benefits for CCP4 in this deal. Paul Swepston agreed there was a conflict between `the Biosym mission' and `the CCP4 mission' and suggested instead that Biosym be granted a licence so that they can develop an interface to CCP4. CCP4 has an established response for such a request and a reply will be sent to Paul Swepston explaining that we encourage companies to provide interfaces to CCP4, and only ask that they purchase a licence. Neil told the WG he had also been approached by Tony Marchington of Oxford Molecular (OM) about arrangements to distribute CCP4. He had sent details of the OM letter to David R., Phil, Eleanor and Sue and arranged for this group to meet OM on the 12th October. The basis of the meeting would be the points discussed at the last WG2 meeting. There was some discussion and Neil was advised to talk to other groups who had dealt with Oxford Molecular. \section{Grant Application for renewal of CCP4} An application for renewal of CCP4 is to be submitted for the February round. Sue asked if we really need to apply for a postdoctoral RA as we can employ programmers from the industrial money. David R. thought that there was still a case for a person on the grant to do development work, and that CCP4 had such a strong case for renewal that we should ask for a PDRA. and it was a good use of research council funding. It was agreed we should ask for a PDRA. Neil asked what developments we want the PDRA to do? Suggestions included: improvements in the programs for phasing and refinement, and work on an interface. The proposal should also stress the role of CCP4 on education, maintenance of existing code, and support to users including documentation to justify continuation of the current support to CCP4.It was agreed that Neil and Sue would write the proposal. \\ ACTION: Neil, Sue \section{Programs} Phil noted that Dave L. had been accumulating programs under the heading V2.10 and asked if a new release were imminent. Dave L. said he had not set a date, but it was agreed that the Daresbury staff would arrange the release of V2.10. \begin{enumerate} \item{} SCALEIT/FHSCAL. David R. noted the minutes of the previous meeting and said they had been having problems with both programs at Sheffield. Fhscal had given less problems than Scaleit and he asked about the old scaling programs. Phil said that the scaling in Scaleit was from Anisosc and was a least squares scale factor plus anisotropic B-factor. Phil pointed out that problems could arise with weighted scaling in Scaleit if the sigmas were not good estimates, in which case unweighted scaling should be done. Problems could also be caused by low resolution reflections behind the backstop or saturated spots. The documentation should be checked to make sure these points are clear. Ian T. said that even taking these factors into account he still thought there was a problem with the algorithm. Phil agreed to discuss this with Ian. Phil recommended scaling derivatives to native using Scala with the native data input as reference data. \\ ACTION: Ian T. and Phil \item{} ROTAPREP. A problem with Rotaprep has bee reported. The output from rotaprep does not contain 3 extra columns now output from mosflm, and this causes problems if the data from rotaprep is to be merged with new mosflm data in rotavata/agrovata. Eleanor and Phil said this problem can be overcome by using mtzutils rather than rotaprep. \item{} NANs. Dave L. had written routines for MTZlib to use NANs to flag absent reflections. However, as no programs yet used them he was thinking of removing them. Implementation requires all programs which read and write MTZ files to be changed to cope with NANs and this is a lot of work. Phil thought it could be implemented so that not all programs had to be changed and described how he thought the routines could be set up. Phil thought it was important to implement use of the NANs. \item{} DM. Kevin has received lots of comments from the first release of DM, some due to problems running on an alpha but that was ok now. DM would be in release 2.10 of CCP4. Feedback on the density modification and averaging suggested that people were very pleased with the results. Kevin was looking into automatic mask generation as an option. New things he intends to try are a diagonal approximation to Sayre's equation, which should speed the program with the same results and extension of the histogram matching. The current work on skeletonisation improves an MIR map, but no more than density modification does. Kevin has looked into doing multiple crystal averaging. It was not easy to set up in an automated way and implementation in other programs involved running parallel jobs talking to each other. He had not yet developed clear ideas on handling crystal forms with no phasing power. Phil said they had been using MAVE for doing this which involves writing long scripts. Kevin suggested putting a message on the BB to find out how many people are interested in doing multiple crystal averaging. Sue asked if we should drop looking into the DEMON/ANGEL package of Fred Vellieux for multi crystal averaging, and it was decided not to do any work on this unless Fred wanted to do it himself. \item{} LOCAL. Ian T. has received several requests to resurrect his local scaling program, and he now has a version which used MTZ files. Some users claimed to find it useful, but some members of the WG felt that it was not a good choice for scaling. Eleanor pointed out that it should be used in P1. She had tried it with the MAD data but had not seen any improvements on other methods. Peter Keller promised to investigate its use at Bath and report back. \item{} MLPHARE. Adam said mlphare was being changed to improve the theory, incorporating ideas from Randy Read and G. Bricogne. Eleanor pointed out that Kim H. had changed many of the variable names to meaningful names which made the program much easier to understand, however others felt this was less helpful as the new names are rather long. Sue asked is anyone had experience of refining sites in special positions with mlphare as this seemed to be causing problems at Daresbury. Eleanor had such data and had not experienced problems and agreed to give Adam some data for him to look at. Eleanor pointed out that if several derivatives have the same site and are refined together with a different derivative this increases the weight from the similar derivatives. This is always true for MAD data. This needs to be put in the documentation. Phil complained that mlphare scrambles the order of the columns in the output file. \item{} RESLICE. New resectioning program from Phil. Uses dynamic memory allocation. \item{} PROTIN dictionary. Eleanor said the default dictionary in \$CLIBD is the old one. Eleanor had run some tests and the John Priestle or Victor Lamzin ones were much better. \item{} PLUTO. Dave L. asked if he could take this out of distribution. Phil said no as NPO still has bugs in it. \item{} XLOGGRAPH. Adam had looked into implementing this on VMS systems, but the program assumes Athena widgets which DEC does not supply. Sheila said she would ask Ian C. if he was interested in looking into this. \item{} Polypose. Sue said she had been approached by Bob Diamond to see if CCP4 wanted to distribute Polypose and Clusterpose and Sue had already received a copy of Polypose. The program superimposes several structures at the same time, but is restricted to each structure (or domain within the structure) having the same number of atoms. It was agreed to distribute the program as unsupported for the moment. \item{} XDLview. Dave L. said there would be a new version of XDLview with the next release. \end{enumerate} \section{Any other business} Jan asked for changes to the method of error reporting for ease of use with ZLDB. He wants error messages to be written to the standard Unix error stream as well as the log file. Dave L. agreed to do this. \section{Venue and date of the next meeting} The next meeting was set for Friday, 9th December 1994 at York Chemistry Department at \mbox{11--30~am}.\vspace{2ex} \noindent ---Sue Bailey (secretary) \end{document}