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\large\bf MINUTES OF THE WORKING GROUP 2 MEETING OF CCP4   
HELD AT YORK ON 6th DECEMBER 1995
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\noindent{\it Present:}  

\noindent
\begin{tabular}{@{}l@{\hspace*{2em}}l}
\\
David Rice (Chairman)           & Sheffield University  \\
Don Akrigg                      & Leeds University \\
Kevin Cowtan                     & York University      \\
Eleanor Dodson                  & York University       \\
Paul Emsley                     & Glasgow University \\
Sheila Gover                    & Oxford University     \\
Paul Holden                     & Bristol University \\
Misha Isupov                    & Exeter University \\
Peter Keller                    & Bath University \\
Peter Moody                     & Leicester University \\
Jim Naismith                    & St. Andrews University \\
Jim Raftery                     & Manchester University \\
Adam Ralph                      & Daresbury Laboratory  \\
Ian Tickle                      & Birkbeck College \\
David Waller                     & Sheffield University \\
Martyn Winn  (Acting Secretary)   & Daresbury Laboratory  \\
\end{tabular}\vspace{2ex}

\noindent {\it Apologies: } Christine Cardin, Peter Daly, Cameron Dunn, Phil Evans, Paul Freemont,
Andrew Hemmings, Neil Isaacs, Gareth Lewis,  Simon Phillips, Richard Pickersgill, Tadeusz Skarzynski,
Steve Yewdall

\section{Minutes of the previous meeting and matters arising}

The minutes of the meeting held on September 6th were approved. There were then several reports
on actions arising from that meeting.

Regarding item~8 of the previous meeting, Peter Keller reported that the mmCIF-handling 
routines had been altered so that several CIF files with the same {\tt data\_} tag could be 
open at once, with each data block being given a unique numerical id.
He hoped that an alpha-release of the toolbox could be made available in January.
\footnote{Although probably no CCP4 programs will have been converted by then.} Since the last
meeting, John Westbrook's SIFLIB software has become available, but this is not distributed as 
source, only as compiled IRIX objects, and it needs the C++ libraries to 
make executables.

Regarding item~9 of the previous meeting,
Eleanor repeated the rationale behind the new treatment of missing data in MTZ
files (now to be represented by IEEE NaNs or VMS ROps), and listed the programs
which needed attention. Multi-record MTZ files were to be left untouched, since 
missing data entries are only important for single-record files.
Programs which only read or only write MTZ files were easy to alter, but those
that both read and write required more attention. Most of these programs have 
been altered in line with the new missing data treatment, but all require extensive
checking before a new release is possible. Martyn described a new jiffy for converting
an old MTZ file, which for example labels a reflection as missing by $SIGF = 0$,
to a new-style MTZ file in which missing reflections are labelled by NaNs.

Regarding item~10 of the previous meeting, the broken {\tt watersort} has been
replaced by {\tt sortwater}. It was decided that the programs {\tt surface} and
{\tt volume} are obsolete and should be moved to unsupported.

Regarding item~11 of the previous meeting, Eleanor reported that Dave Love had still
not received a copy of the `MR tutorial' from Paul Hempstead. The original, apparently
sent to Sue Bailey, has still not been located.

Eleanor reported that she still had problems with the forthcoming article
in {\sl Methods in Enzymology} on the CCP4 suite. She has agreed to do the
article but does not have time to do it single-handed. The article is wanted asap, but
the end of February would be a reasonable deadline. The article will consist
of an overview of the methods, a description of the data formats used and a summary
of how the programs tie together (probably using flow charts). Most of this can be
taken verbatim from the manual. It was agreed that Eleanor would decide exactly
what material should be included, but that she should have help producing the manuscript
and in proofreading it. Sheila offered to work the LaTeX source of the manual into a
suitable MS. David Rice suggested that at least 6 people should volunteer or be volunteered 
to proofread sections of the article. Ian, Jim Naismith, Kevin, Peter Keller, Paul Emsley,
David Waller and Paul Holden volunteered.

Sheila asked if copies of the referees comments on the BBSRC grant renewal application
were available. Adam has these, and copies will be sent out with the minutes.

\section{New working group members}

Adam welcomed Peter Moody and Jim Naismith as new members of WG2. Another new member,
Andrew Hemmings (UEA), was unable to attend.

The suggestion that the somewhat isolated Irish groups should be invited was discussed
again. David Rice asked if CCP4 could afford the additional travelling expenses. It was
suggested that a single representative for Ireland should be invited, and that he or she
should be invited for more than a single day. Adam\action{Adam} will send out a letter
soliciting nominations for the Ireland representative.

\section{Study Weekend 96}

Eleanor handed out a tentative program for the Study Weekend. A general discussion
has been added to the end of the programme, at the expense of shortening some
of the talks.

Adam said that
385 applicants had been accepted, with 50 more on a waiting list. This is
the first year to be oversubscribed at Chester. The restriction on the numbers
arises from the number of rooms available in Chester College and from the
size of the lecture hall. Of those on the waiting list, 25 were from abroad.
David Rice noted that encouraging applicants from the EU would help with EU-funding.
It was decided that Adam and Eleanor \action{Adam,Eleanor}
should try to fit in some of the applicants on the waiting list, possibly using
hotel accomodation. Institutions which were already sending a large contingent could be 
asked to withdraw some applicants.

There was then a general discussion on future Study Weekends. Either restrictions
on numbers should be applied, or a larger venue should be sought. The Daresbury
Conference Office would probably be willing to organise the Study Weekend at a different
venue, but the meeting was reminded that from next year they will charge for their
services (the fee has not yet been fixed, Adam will enquire\action{Adam}). It was suggested 
that a University conference office might be cheaper than Daresbury. Eleanor said that
York had facilities for up to 450 people. It was decided that enquires should be
made on the facilities that different universities could provide, and Adam would
write a letter to the members of Working Group~1 asking them to enquire at their
universities \action{Adam}. A potential problem might be overlap with the beginning
of the university term. Meanwhile, in view of the advance notice that Chester College
requires, it was decided to opt again for Chester College for 1997.

A suggestion to video the Study Weekend was not greeted with enthusiasm.

\section{CCP4 Workshops}

Keith Wilson has funds for a workshop on Molecular Replacement to be held in September. 
60 students from the EU have applied. Phil Evans also has money to hold a workshop,
but the details are yet to be finalised.

Adam noted that there is a Macromolecular Crystallography Computing School scheduled for
17th -- 22nd August 1996 \footnote{For further details, see
http://www.sdsc.edu/Events/IUCr/IUCr.html}, following on directly from the IUCr Seattle 
meeting, and that tutorials on the CCP4 software are included in the tentative programme.
Phil Bourne had asked Eleanor and Phil to represent CCP4, but they were as yet undecided.
In view of the fact that other software packages were to be represented, it was agreed
that CCP4 should send someone. David Rice thought that the CCP4 budget would stretch
to three people, with complementary skills. Adam was asked to find out more from Phil
Bourne as to what was required \action{Adam}.

\section{CCP4 organisation}

David Rice handed out a sheet summarising the meeting at Daresbury on 1st November
at which changes to the CCP4 management structure were proposed. A central element
of these changes is the creation of an executive committee of WG1 which will have
the power to make decisions quickly. It is intended that this committee will deal
with most financial matters, leaving WG2 to concentrate on matters connected
with the program suite. 

It was also decided at the Daresbury meeting that there should be elections every
3 years for the Chair positions of WG1 and WG2. In this connection, David Rice will
shortly yield up his position as Chairman of WG2, and nominations for a replacement
are sought. Adam will write a letter to this effect to be sent out with the minutes
\action{Adam}. To date, the only nomination is Phil Evans, who has agreed to be
considered. It is hoped to make a decision before the next WG1 meeting in January.
Sheila asked who would be eligible to vote for the Chairman. David Rice replied
that the mechanism for elections would be decided by the Chairmen of WG1 and WG2.

\section{Report on CCP11 meeting / DISguISE}

Martyn described the CCP11 meeting held at UCL on 25th October at which a GUI named
DISguISE was presented. DISguISE is intended to form a common graphical interface
to the programs available via SEQNET. For each program, windows are created allowing
selection of input files and parameters, and allowing easy viewing of output data.
Checks on input data and help information can be easily incorporated. In addition,
a menu window is available from which to choose appropriate programs. Output file
icons can be dragged into the input area of subsequent programs.

DISguISE was created by Tom Flores and developed at Daresbury for CCP11 by Yasmin Khan.
CCP11 would be delighted for CCP4 to adopt DISguISE, and there should be no licensing
problems. DISguISE scripts are written in TCL/TK and some work would be needed to adapt these
to CCP4 programs (Martyn has so far created very simple prototype tools for {\tt npo} and 
{\tt procheck}). DISguISE is certainly less sophisticated/ambitious than other GUIs considered,
but might therefore be realisable. Problems which need to be addressed are dealing with
the variable parameter input typical of CCP4 programs, and linking a series of programs
together as is done in unix/VMS scripts. It was suggested that a comparison with ZLDB 
should be done \action{Martyn, Paul Emsley}.

\section{Programs}

\begin{description}
\item[{\bf solomon}] Adam confirmed that {\tt solomon} will be present in
the next release of the CCP4 suite. Changes have been made to make {\tt solomon}
more CCP4-like, and the question was raised as to how far the program had diverged
from Jan-Pieter's original. It was suggested that there should be discussions with
Jan-Pieter on this, and that he would appreciate some feedback.
\item[{\bf SkulD}] Ito is willing to give the code to CCP4 but this will need
some work. Apparently, Ito will return to Japan soon, so that work should be done
on the code asap. David Waller reported that {\tt SkulD} still requires
conversion to use CCP4 libraries, portability checks and documentation. He will try
to get it working on his Alpha \action{David Waller}. The advantage of {\tt SkulD}
over other programs is in its handling of chickenwire density.
\item[{\bf geomcalc}] Adam confirmed that {\tt geomcalc}, created by Phil Evans,
will be available in the next release. David Rice asked how it differed from
{\tt procheck}. Eleanor replied that {\tt geomcalc} can be used to define
planes, and to calculate distances and angles from this plane.
\item[{\bf PDBtool}] Phil Bourne has made a number of programs available
via the San Diego Supercomputer Centre ftp site\footnote{See
http://www.sdsc.edu/CompSci/pb/Software.html}, and has said that these could
be distributed with the CCP4 suite. One program which may be of particular interest
is PDBtool which displays a rotatable/translatable view of a protein. Different elements
of the structure may be selected, and various lengths and angles calculated.
The functionality is not as good as {\tt procheck}, but the presentation is
excellent. Considering the slowness of the trans-Atlantic link, it was thought
important that any programs aggregated to CCP4 should be distributed from Daresbury.
The possibility of setting up a mirror site at Daresbury for Phil Bourne's programs
was raised. Martyn was asked to sound Phil out on this\action{Martyn}.\par\indent
The issue of a mirror site for the CCP4 suite in the U.S. was raised again.
It was suggested that Phil Bourne would be an ideal candidate to host such a site.
Working Group~1 will discuss this further.
\item[{\bf Additions/deletions}] Eleanor has added a COMPLETE option to
{\tt freerflag} which will complete an existing list of FREE flags when extending
the indices.
\end{description}

Don asked when the next release was due. Adam replied that this was uncertain,
since it depended on how quickly the missing data treatment could be finalised. There was
then a short discussion on the availability of program fixes. Major fixes are
available via the prerelease directory in the ftp area and are advertised via the
Bulletin Board. It was suggested that there should be individual version numbers
for each program and that the latest versions should be available, but it was felt
that this would be more confusing than the present system.

\section{Any other business and date of next meeting}

As of 1st December, Dave Love has taken up a new post at Daresbury in the Data Acquisition
section. The meeting recorded its thanks to Dave for his invaluable contribution to
the success of CCP4. A gift was signed by those present.

Peter Moody raised the issue of support for installation problems, in particular with
regard to interference between simultaneously-installed program suites. It was reiterated
that such problems should be referred to ccp4@dl.ac.uk. Eleanor suggested that someone
write a short guide to installation issues, but there were no volunteers. It was felt
that different systems were too diverse. 

It was asked whether the CCP4 suite had ever been ported to a PC running the LINUX OS.
It was thought that this should be possible, but no-one had attempted it. 
\footnote{We have since heard that Vinay Kumar has successfully ported the CCP4
suite to a Pentium-60 PC with 16MB of physical RAM running LINUX OS. Further details
can be obtained from ccp4@dl.ac.uk}

The next meeting was set for Wednesday February 21st, at Birkbeck.

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