\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 1st MARCH 1995 \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 \\ 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 \end{tabular}\vspace{2ex} \noindent{\it Apologies: } Neil Isaacs, Cameron Dunn, Simon Phillips \section{Minutes of the previous meeting and matters arising} The Chairman welcomed the members and in particular Paul Hempstead, who is working for CCP4 for 3 months, and Tadeusz Skarzynski, the new industrial representative. The minutes of the meeting held on 9th December were agreed. With respect to a further person to work on CCP4, agreed at the last meeting, Sue reported that Peter Lindley and Neil Isaacs had agreed and that the personnel department at Daresbury had been approached and the matter had been sent to the head of DRAL for approval. Don thanked the Daresbury staff for setting up the prerelease directory and said he found it excellent. Phil agreed with this. Eleanor reported on progress on the free $R$-factor workshop and asked for a CCP4 representative to attend. Peter Keller agreed to ask Garry Taylor if he would attend. \section{ Study Weekend 95} Sue reported that the there had been no outstanding administrative problems. The collection of articles for the proceedings was going well with 11 out of 16 expected contributions received so far. \section{ Study Weekend 96} The chairman said that WG1 had suggested a study weekend on refinement and Eleanor had volunteered to be an organiser. There was some discussion of whether refinement had been covered in recent meetings but the conclusion was that there were many new ideas that needed discussion. A younger scientist was suggested as a co-organiser and Eleanor suggested Madeline Moore at York who also has expertise in DNA refinement. Eleanor described the topic headings she thought would be appropriate and some potential speakers were suggested. Topics were: \begin{enumerate} \item New Algorithms -- ideas from free $R$-factor workshop, use of maximum likelihood instead of least squares residuals, use of F$^{2}$ or Is instead of Fs. Refinement in torsional space. \item Restraints and how to use them -- defined as bonds, angles and planes or as energy terms. How to build a new ligand. \item Error estimates and weighting between crystallographic data and restraints. \item Scaling -- this is related to solvent and depends on the refinement protocol. \item Reporting structure quality -- $R$-factor, free $R$-factor, $w\Delta^{2}$. \end{enumerate} Phil also suggested something on the modelling of motion and alternative conformations. After discussion, the group agreed that the study weekend should be held at Chester College at the same time of year. Sue confirmed that Chester College is available and provisionally booked for the 5/6 January '95. There was some discussion about the size of the meeting and whether numbers should be restricted. No decision was made, however, holding the meeting at Chester will not allow a significant increase in numbers over 1995. Action: Eleanor, Madeline \section{Finances} Sue said these had not really altered from the previous meeting. The question of money carried forward at year end was raised. Sue did not foresee any problems, in spite of the changed status of Daresbury Laboratory. \section{Grant application for renewal of CCP4} David R. summarised the current position. A grant proposal has been written and circulated to various people for comments. The grant requests support for 2.5 people, and the programme of work includes maintenance of software, support of the collaborative nature of the project, and development of software. Action: Sue \section{Programs from M. Rossmann } An email from Michael Rossmann (enclosed) offered the Purdue programs for distribution by CCP4. The programs cover many of the same functions as CCP4 but are optimised for large unit cells. Some versions of the programs are highly specific to certain computers and are not useful to us. Also some programs developed by L. Tong, eg.\ Patterson search are not available to us at the moment. There was some discussion of whether it would be useful to use some of the programs. It was agreed that it would be good if the CCP4 suite was able to handle virus problems. It was agreed that a letter be sent to Michael and Liang stating which programs we were mainly interested in and asking if we could have access to all programs. Also Kevin and Sheila would try to persuade the Oxford virus group to check out the feasibility of using DM for averaging virus structures. Action: Sue, Kevin, Sheila \section{Priorities for development} The chairman explained that WG1 felt there was a need to identify gaps in the suite and priorities for development in order to ensure that the industrial income was used to fund software development in an efficient manner. Sue had circulated various ideas with the agenda and these were intended to stimulate discussion. The ideas were: protein refinement, rewrite FFT routines, improve (rewrite) mlphare, develop GUI (zldb), include graphics, better Patterson search program, DM development, molecular replacement and CIF\@. These ideas were discussed in turn. \begin{enumerate} \item{} Protein refinement. It was agreed that we need something better than Prolsq and Garib is already working on such a program. Alexei Vagin is also involved in this work and it was agreed that we should approach him to see if he would like to be supported by CCP4 to do some work in this area. \item{} CIF\@. We will need a conversion program between CIF and PDB and also library routines to replace rwbrook. This is enough to allow programs to read and write CIF files. It was noted that not all programs currently use rwbrook. Changes will also be needed to various programs (eg Agrovata, Mlphare refinement) to write out data which can be incorporated into CIF files. Eleanor said that the definition of atom records in the CIF format was now completed and was unlikely to change. A program to convert PDB to CIF is available from the PDB. \item{} Rewrite FFT routines. Phil questioned if this needed to be done. Dave L. pointed out that the existing routines used illegal Fortran, and will potentially cause problems with some compilers. Dave L. had written to Lynn Ten Eyck who has produced updated routines, although not to remove this problem. Lynn said these routines are freely available but so far has not responded to a request for the routines. This work was not thought to be a top priority. \item{} Improve/rewrite Mlphare. Adam has been looking into incorporating potential improvements into Mlphare. This work was felt to be lower priority than protein refinement. \item{} GUI/Zldb. There was some discussion about whether development of a GUI was a priority. Zldb was felt to be difficult to start using. The general feeling was that the WG did not know what they wanted from a GUI and so were unable to specify what development should take place. \item{} Graphics. Kevin noted that programs providing graphics could be very useful, for example, for looking at the masks generated by DM\@. Jan Zelinka had incorporated such graphics into Zldb, although during development they had been used as stand-alone programs. These graphics use GL, and could be used from SGI consoles only. Given the perceived difficulty in using Zldb, it was suggested that we ask Jan to set the graphics up to be used separately from Zldb (and port the graphics to X?). \item{} DM\@. Kevin gave a short description of the work he had done since the last meeting. He has written programs Mapmask and Ncsmask, implemented the skeletonisation code and multi-crystal averaging. The work Kevin is doing was given a high priority, although it is unlikely to need further funding from CCP4 if a grant was awarded by the BBSRC. \item{} Patterson search program -- something better than Rsps. Eleanor said that people should be using Shelx90. However, other members complained that this is not yet available, and there are few signs that it will be in the near future. Eleanor said she would have a word with G. Sheldrick to try and persuade him to release it. \end{enumerate} The list of priorities was then agreed as: \begin{enumerate} \item DM -- ensure development continues. \item Prolsq replacement -- Garib to talk on progress at next WG2 meeting, approach Alexei Vagin about working in this area. \item Graphics -- ask Jan if we can use the graphics he has incorporated into Zldb as a stand alone function. \item CIF \item Mlphare \end{enumerate} \section{Documentation Standards} There was some discussion on the best format for master copies of the documentation, currently \LaTeX{} for the `CCP4 Overview and Manual' and nroff for the program documentation. One possibility is conversion to HTML\@. There was no enthusiasm for changing at the present time. The one feature that was generally thought to be important was that a plain text version should be available. It was agreed that Paul Hempstead should start on the FAQ list, using Dave Love's list as a starting point. He should also work on the tutorial and perhaps convert a few program documents from man to HTML as a trial. \section{Programs} \begin{enumerate} \item{} Scala/Rotavata. Eleanor agreed to the removal of Rotavata from the suite. However, it was pointed out that Scala does not write a file suitable for input to Postref, and until this is implemented Rotavata should be retained. Action: Phil \item{} Envelope/Flatmap. Kevin to check that all functions are replaced by DM and associated programs and check with Andrew Leslie prior to removal from the suite. \end{enumerate} \section{Any other business} Ian Tickle suggested that we ask Roman Laskowski about distributing Promotif (program to analyse structural motifs) with CCP4. David Waller asked when 2.14 would be released. It is intended to release 2.14 within the next few weeks, as soon as matters arising from the current meeting had been resolved. Dave Love asked if he should include the latest version of Procheck, and if so, which parts. It was agreed that he should include Procheck and Procheck\_comp, but not Procheck\_nmr. Sue said that she would not be attending the next meeting as she is expecting a baby on 30th June and will be on maternity leave from the end of May, probably until January '96. \section{Venue and date of the next meeting} The next meeting was set for Wednesday, 7th June 1995 at York Chemistry Department at \mbox{11--30~am}. \vspace{2ex} \noindent ---Sue Bailey (secretary) \end{document}