\documentclass[a4paper,11pt]{article} %\usepackage{times,mathptm} \newcommand{\action}[1]{\marginpar{\flushleft {\bf Action}: #1}} %\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}{1.0in} \textwidth 13.0cm \oddsidemargin 0.0cm \evensidemargin 0.0cm \begin{document} \begin{center} \large\bf MINUTES OF THE WORKING GROUP 2 MEETING OF CCP4 HELD AT YORK ON 22nd JANUARY 1997 \end{center}\vspace{5ex} \noindent{\it Present:} \noindent \begin{tabular}{@{}l@{\hspace*{2em}}l} \\ Phil Evans (Chairman) & MRC, Cambridge \\ Sue Bailey (Secretary) & Daresbury Laboratory \\ Jim Naismith & St. Andrews University \\ %Don Akrigg & Leeds University \\ %Peter Daly & ESRF Grenoble \\ Eleanor Dodson & York University \\ %Mike Hartshorn & York University \\ %Gideon Davies & York University \\ %Cameron Dunn & Bristol University \\ Paul Emsley & Glasgow University \\ Roger Sayle & Glaxo Wellcome \\ Liz Potterton & York University \\ %Neil Isaacs & Glasgow University \\ Sheila Gover & Oxford University \\ Paul Holden & Bristol University \\ Peter Keller & Bath University \\ Adam Ralph & Daresbury Laboratory \\ Martyn Winn & Daresbury Laboratory \\ %John Campbell & Daresbury Laboratory \\ %Sandra McLaughlin & Hamburg \\ %Simon Phillips & Leeds University \\ Jim Raftery & Manchester University \\ %Peter Brick & Imperial College \\ Ian Tickle & Birkbeck College \\ %Jan Zelinka & York University \\ Kevin Cowtan & York University \\ %Tom Flores & EBI \\ David Waller & Sheffield University \\ Garib Murshudov & York University \\ Yao Jia-xing & York University \\ %Tadeusz Skarzynski (Industrial rep) & Glaxo \\ %Steve Yewdall & Edinburgh University \\ %Ian Clifton & Oxford University \\ %Paul Hempstead & Sheffield University \\ Misha Isupov & Exeter University \\ %Paul Freemont & ICRF \\ %Andrew Hemmings & UEA \\ %Gareth Lewis & Southampton \\ Christine Cardin & Reading \\ %Tim Higgins & Galway \\ %Joe Jaeger & Leeds \end{tabular}\vspace{2ex} \noindent{\it Apologies: } Paul Freemont, Tadeusz Skarzynski, Gareth Lewis, Andrew Hemmings, Joe Jaeger \section{Minutes of the previous meeting and matters arising} The minutes of the previous meeting were agreed. Phil reiterated that installation of the X-Windows programs should be automated. Adam and Martyn replied that they intended to look at this when they had time.\action{Adam,Martyn} Adam said that he was working on making the shared library option work on more systems. Phil wished it noted that he was still concerned at potential problems if the PDB and mmCIF formats were run in parallel. This had been discussed at the previous meeting. \section{Welcome to new CCP4 staff} Garib Murshudov, Liz Potterton and Yao Jia-xing were officially welcomed. Garib has a 3-year contract funded by the BBSRC grant to continue his work on {\tt refmac}; Liz has a 2-year contract funded by industrial money to implement the CCP4 GUI; and Yao has been funded for 6-months from industrial money to continue his work on phasing MAD data. Alun Ashton will start work at Daresbury in mid-March on a 2-year contract funded by industrial money. \section{Estimating the anomalous contribution FA for MAD data sets.} Yao gave a short presentation on his method for phasing MAD data. His target was structures with up to 20--40 heavy atoms. Eleanor made a request for good unmerged data for testing the procedure. Ian asked whether a maximum likelihood approach would be better, but Eleanor said that was difficult. \section{{\tt refmac} --- recent progress and planned developments} Garib described the error estimation {\it \`a la} Cruickshank (see current Newsletter) which he has incorporated into {\tt refmac}. He gave the following list of future development projects: modelling of solvent shells and replacement of bulk solvent correction; anisotropic scaling; rigid body refinement; anisotropic B-value refinement; inversion of full (block) matrix to get e.s.u. for each parameter. \section{GUI update} Liz described her progress so far and demonstrated a simple ``GUIlet'' for running {\tt dm}. Liz favours using Tcl/Tk to implement the GUI: Tcl/Tk is popular, relatively simple to work with, and should be portable to all relevant systems. Liz and David Waller are to confirm as soon as is feasible that Tcl runs OK on VMS systems.\action{Liz, David~W.} At the moment, the GUI is used to prepare a unix script which then runs the program. An edit button allows the experienced user to alter this script before running it. At the separate meeting of the WG2 sub-group overviewing GUI development, it was suggested that a portable generic scripting language be used. Liz will investigate these possibilities, and also look at the ZLDB template scripts. The choice of a suitable program for 2D-graphics was discussed, in particular {\tt gnuplot} (not GNU apparently) or {\tt xmgr}. {\tt rasmol} was included in version 3.2 of the Suite. Development requests were that it should display electron density (priority) and should be able to display more than 1 set of coordinates (either side-by-side or superimposed). \section{Study Weekend 1998} This will be on databases, with the emphasis on what's available for crystallographers rather than design issues. The organisers will be Judith Murray-Rust and Liz Potterton.\action{Sue} The date and venue is still uncertain. York would be available for the 23rd/24th January, but accomodation would have to be in local hotels. Alternatively, York could host the Study Weekend at Easter, but this was felt to be in conflict with the BCA meeting in St. Andrews. The best option seemed to be 9th/10th January at Reading. There is a limit of 400 on the lecture theatre, but an overflow room would be provided. Sheffield and Leicester were also possible, though it was unclear whether the lecture theatres would be suitable. Sheffield was possible on the 9th/10th January. Sue is to investigate Reading and Sheffield and make a decision. \action{Sue} \section{CIF update} Sue said that Adam was going to work with Peter K. to get the CIF routines implemented. Phil asked how close we are to having a set of routines we can plug into any program. Peter K felt he had a little more work to do which would be finished probably by the end of February. First priority was to get a program to convert from PDB to CIF and vice versa (best done as options in {\tt coordconv}).\action{Peter~K, Adam} \section{Data Harvesting} Peter K. described recent work at the EBI on extracting deposition information from programs used in structure solution at the time they are run, rather than {\it a posteriori} (see Kim Henrick's message, enclosed). The idea was that programs such as {\tt scala} would create files at run-time containing information to be included later with the deposition of final co-ordinates. Time- and project-stamps would be included to help identify the file; Phil suggested a third stamp to distinguish between different processing routes. There was some discussion as to whether this information could be held in the datafile header rather than as separate files. The EBI would provide subroutines for outputting the necessary data, but their inclusion will be easier when the mmCIF format has been included in the Suite. Overall, the response was favourable, and the EBI will pursue this further. \section{{\tt sfcheck}} {\tt sfcheck} is part of Alexei Vagin's BLANC suite, and gives various statistics on the agreement between a model structure and the observed structure factors. The program was thought to be useful, and Martyn will ask if we can include it in the next release \action{Martyn}. A number of modifications will be suggested, such as reading MTZ files directly, and replacing the Luzzati plot with Cruickshank's DPI parameter. Martyn will also look at two further programs from the BLANC suite, namely {\tt molrep} and {\tt mir}. \section{Changes to the suite} \indent {\tt scala} --- current version 2.2.2. An article describing this is in the current Newsletter. It should be picked up from Cambridge and distributed in the prerelease directory.\action{Adam,Martyn} {\tt arp} --- CCP4 now have program and examples but no documentation as yet. The program will be released in the next version. \section{ccp-dev mailing list} This was originally set up for developers to discuss technical points not suitable for ccp4bb, but is hardly used now. It was felt that it could be useful, and should be revived. The list is being moved to a new server; when that is done, Adam will add WG2 members to it and then advertise its availability.\action{Adam} \section{Any other business} WG1 had suggested that CCP4 sponser small (15--20 people) workshops. Two suggested topics were MAD and refinement. It was suggested that Jim Naismith and Eleanor organise a refinement workshop this year. Jim presented a proposed programme and costing for a workshop to be held in York in July/August; total cost approx 11K. WG2 agreed to the proposals and Jim is to finalise them for submission to the CCP4 executive committee.\action{Jim N.} Eleanor announced that Dave Stuart had made an offer to contribute software to CCP4. In particular, averaging programs were discussed. Sue is to approach Dave Stuart about this.\action{Sue} Neil Isaacs had suggested that CCP4 should have a logo, for adding to letterheads, the Web page, etc. Martyn will investigate this, and seek suggestions.\action{Martyn} \section{Venue and date of the next meeting} The next meeting was set for {\bf Thursday 24th April} at Birkbeck, starting \mbox{11--30~am}. \end{document}