% % Macros for JMB papers % \def\Ang{\thinspace\AA} \def\Angsq{\Ang$^2$} \def\percent{\thinspace\%} % \magnification = \magstep1 \font\bfbigten=cmbx10 scaled\magstep1 \font\bfbignine=cmbx9 scaled\magstep1 \font\itbigten=cmbxti10 scaled\magstep1 \font\scbig=cmbx7 scaled\magstep1 \font\sc=cmr7 \font\scl=cmr7 scaled\magstep1 \hoffset .46 true cm \voffset .46 true cm \hsize 16.0 true cm \vsize 23.0 true cm % % \baselineskip=12pt \normalbaselineskip=12pt % \outer\def\section#1\par{\vskip0pt plus.3\vsize\penalty-250 \vskip0pt plus-.3\vsize\bigskip\vskip\parskip \message{#1}\centerline{\bf#1}\nobreak\smallskip} % \outer\def\subsection #1 #2\par{\medskip\centerline{#1 \it#2}\nobreak\smallskip} % \outer\def\subsubsection #1 #2\par{\medskip\leftline{#1 \it#2}\nobreak\smallskip} %\raggedright \centerline{\bf MINUTES OF A MEETING OF WORKING GROUP 2 OF CCP4} \centerline{\bf WHICH WAS HELD AT BIRKBECK ON 3rd May 1989} \bigskip \noindent Present: \medskip $$\vcenter{ \halign{#\hfil&\qquad#\hfil\cr David Rice (Chairman)&Sheffield University\cr David Moss &Birkbeck College\cr Don Akrigg &Leeds University\cr Eleanor Dodson &York University\cr Phil Evans &MRC, Cambridge\cr Ian Tickle &Birkbeck College\cr Sandra McLaughlin &EMBL Hamburg\cr Jan Zelinka &York University\cr Garry Taylor &Oxford University\cr Paul Mallinson &Glasgow University\cr Kim Henrick (Secretary)&Daresbury Laboratory\cr }}$$ \bigskip {\rm {\it 1. The minutes of the meeting of 17th February 1989 were agreed.} \bigskip {\it 2. Matters Arising} \medskip With reference to item 4 of the minutes of 17th February 1989 the chairman reported that he had had further contact with group leaders about contributions to the Information Quarterly for Protein Crystallography, and that the tone of some of these replies were discouraging for the future of this newsletter. The chairman stressed the informal nature of the newsletter the members of the committee were in support of the continued publication. Owing to the delay in receiving contributions the deadline for the next issue has been now set to be the end of May. The secretary informed the meeting that the RA post for CCP4 at Daresbury laboratory had been offered to a Mr Peter Daley who was expected to start on the 3rd of July. \bigskip {\it 3. The 5-Year Forward Look for SRS Computing Requirements at Daresbury Laboratory} \medskip The secretary reported on the decision taking place at Daresbury on the future of computing resources at Daresbury. A plan had been submitted for consideration to the staff at Daresbury in which Unix based systems were planned to completely replace VMS within 5 years. The PX project team had submitted a counter proposal that there was a clear need for a Dec VMS computer at least of a workstation with enough memory and disk space to support and maintain the CCP4 collection. However, this may not be a general access machine and both local and remote users will be encouraged to use either the Convex or the Sun 3/60 network. (This will only affect a small number of users, particularly from, Keele, Manchester, Liverpool, and possibly Birkbeck and Oxford, and any replacement machine is not intended to be a distributive computing system.) \bigskip {\it 4. The 1990 Study Weekend on Accuracy and Reliability of Macromolecular Crystal Structures} \medskip David Moss joined the meeting and presented a draft of a possible agenda for the 1990 Study Weekend. (A copy is attached). The arrangement of the group topics into sessions that would fit into the Study Weekend formula was discussed and apart from invited speakers, David Moss also suggested that time could be set aside for individuals to present 2 or 3 slides for 5 to 10 minutes in support of a particular topic. There was some discussion of the details of the proposed outline as to how much time could be spent on each grouping of items and doubt was expressed that groups 4 and 5 (see attached list) should merit a session each. It was felt that item 7 on Databases should be given more time at the expense of the consideration of errors in electron density maps and the interpretation of electron density maps (items 4 and 5). Several additional points were raised that were thought merited inclusion in the timetable. These included (1) uniformity of samples; (2) bugs in programs; (3) partial data sets; (4) cell dimensions. The overall view appeared to be that speakers should be sought who could present from experience the practicalities of protein structure determination through case studies. Several overseas speakers names were suggested and David Moss and Ian Tickle agreed to contact these individuals. ( The date for the 1990 Study Weekend has been booked at Daresbury for the 26th and 27th of January and a hotel booking with the Crest has been made). David Moss also asked the committee members for suggestions for speakers from within the U.K. for any of the topics listed. \bigskip {\it 5. Molecular Replacement Programs} \medskip Phil Evans indicated that he was preparing an overview of the available molecular replacement programs and felt that there was a need to bring these programs into a more consistent set. He also thought that although MERLOT was being recommended as the definitive program, his experience was that structures solved with MERLOT were equally solved with TSEARCH and TFSGEN. The question was, is a new user guide complete with test data necessary and who was going to do it. Eleanor Dodson informed the meeting that she had a version of MERLOT that included PDB and LCF files. It was also reported that just as TSEARCH had an error for hexagonal space groups that this same error was reported to be present in MERLOT by the workers in Bristol. It was felt that a new version of CADLCF was required and that work should be undertaken on the keyworded version of ALMN. \bigskip {\it 6. Design of a uniform Multipurpose Flexible File Header System} \medskip Jan Zelinka was invited to the meeting to describe the work he had carried out at York on the design of a header system written in Fortran 77. He described a header system as a sheet of paper of given length and width that was identified by a unique readable name. Each header consists of a header name (belonging to a particular class of header) followed by a set of textlines containing free format keyworded entries. A set of basic operations were supported in, creating a header of given properties, delete a header, write to a header, read from a header, rewind a header, flush a header, rename a header, copy a header, append headers, delete entries within a header. He further proposed that any work on keywording be extended to parse information from the headers if compulsory input was not available from the standard input unit. This information could either be got from the data file headers or from a project or history file of constants related to the protein under study. There followed a discussion on the merits of this system and what was required for CCP4 data files. There was disagreement over how the planned LCF routines with the proposed flexibility in user (or site, or machine dependent) control of the data structure could be accommodated by a general sorting procedure. The meeting ended split over the type of headers required for CCP4 and the degree of flexibility that was to be allowed for the data types to be stored. PRE and SM favoured a flexible data structure and an inflexible non-ascii header while EJD and JZ favoured the ascii header system an an inflexible all reals data structure. There was also a discussion of the way to treat Batch headers in the new LCF routines with KH, EJD and JZ supported the ascii header system (modified to allow for variable length headers, and headers to be placed at the end of files). \bigskip {\it 7. Use of LCF files} \medskip Paul Mallinson raised a question of how does an inexperienced user of CCP4 create an LCF file from a card image of data. This was quickly answered by the more experienced users of CCP4, but demonstrated that the CCP4 package needed an overall plan to introduce new users to the large number of programs, command procedures and documentation files. It appears to be a common problem of new users to the system that of where to start to get to grips with the program suite. \bigskip {\it A date for the next meeting was set for Wednesday the 19th of July 1989 at York for 11-30 am.} \bigskip \medskip \centerline {K. Henrick} \centerline{(secretary)} } \vfill\eject \centerline {\bf CCP4 STUDY WEEKEND, JANUARY 1990} \bigskip \centerline{\it Accuracy and Reliability of Macromolecular Crystal Structures} \medskip $$ \vcenter{ \halign{ \bf#\hfil\quad& #\hfil\cr \noalign{ \noindent {\bf 1. Theory of Errors} \smallskip} a)&Random versus Systematic Errors\cr b)&Independent and Correlated Errors\cr c)&Propagation of Error\cr d)&Error Distribution\cr e)&Hypothesis Testing\cr \noalign{ \medskip \noindent {\bf 2. Coping with Systematic Experimental Errors} \smallskip} a)&Properties of error--free data\cr b)&Absorption -- short wavelengths, small crystals,\cr & dataset scaling\cr c)&Radiation damage -- monochromatisation, high--\cr &intensity sources, crystal cooling, chemical\cr &modification\cr d)&Use neutrons -- random errors more important\cr \noalign{ \medskip \noindent {\bf 3. Errors in Phase Determination} \smallskip} (i)&Isomorphous replacement and anomalous scattering\cr &(a) Random -- small intensity differences\cr &(b) Systematic -- lack of isomorphism\cr (ii)& Molecular Replacement\cr &(a) Errors due to imperfect probe --\cr &\quad differences due to crystal packing,\cr &\quad lack of sequence homology\cr &(b) Errors due to thermal parameters\cr \noalign{ \medskip \noindent {\bf 4. Errors in Electron Density Map} \smallskip} a)&Consequences of errors in phasing --\cr & heavy atom ghosting and distortion\cr b)&Consequences of radiation damage\cr }}$$ \vfill\eject $$ \vcenter{ \halign{ \bf#\hfil\quad& #\hfil\cr \noalign{ \noindent {\bf 5. Interpretation of Electron Density} \smallskip} (i)&Low Resolution\cr &(a) Chain tracing errors\cr &(b) Errors in recognition of secondary structure\cr (ii)&High Resolution\cr &(a) Errors in orientation of\cr &\quad peptide planes\cr &(b) Errors in identification of side chain --\cr &\quad errors in or ignorance of sequence\cr &(c) Errors in positioning side chain --\cr &\quad confusion with solvent density\cr &(d) Errors in interpretation of water and\cr &\quad ion positions\cr &(e) Errors in modelling disorder\cr \noalign{ \medskip \noindent {\bf 6. Errors Refinement} \smallskip} a)&Errors due to false minima\cr b)&Errors in modelling disorder -- anisotropic and\cr &\quad anharmonic disorder\cr c)&Significance of standard deviations\cr d)&Errors in modelling solvent\cr e)&Use of omit maps in quality control\cr \noalign{ \medskip \noindent {\bf 7. Quality Control in Co--ordinate Databases} \smallskip} a)&Errors in stereochemistry -- wrong chirality, incorrectly\cr &\quad restrained interatomic distances\cr b)&Errors in assignment of secondary structure\cr c)&Measures of quality -- resolution, R--factors etc\cr d)&Assignments of hydrogen bonds and ionic interactions\cr }}$$ \bye