Uppsala Software Factory - Did you know ?

• In February 1998, the Uppsala Software Factory was at the Institute of Molecular Biophysics of Florida State University.

• And this is what Lynn Ten Eyck once said in the newsgroup bionet.crystallography:

  
  Subject:      Re: b-factor refinement
  From:         "Lynn F. Ten Eyck" 
  Date:         1997/03/13
  Message-ID:   <3328F0AC.496D@sdsc.edu>
  Newsgroups:   bionet.xtallography
  
  Howard Flack wrote:
  > 
  > Ask Lynn van Eyck.
             ^^^
        Lynn Ten Eyck, actually.
  
  There is an excellent discussion of refinement practice by Kleywegt and
  Jones to come out in "Methods in Enzymology", but in the mean time
  available at http://alpha2.bmc.uu.se/gerard/gmrp/gmrp.html -- and I
  strongly recommend that you download this while you can.  It doesn't so
  much contain explicit cookbook advice on when to refine what as it does
  advice on how to tell if what you have done is appropriate for your
  data.  This is actually the correct problem to address.  The approach
  relies heavily on Rfree.
  
  The same server used to have a copy of the Kleywegt & Jones Structure
  article,  Gerard J Kleywegt and T Alwyn Jones: Where freedom is given,
  liberties are taken [Ways & means] Structure 1995 3 : 535-540 which has
  to be one of the more enjoyable diatribes I have read in a long time. 
  Alwyn and Gerard would have done very well as Old Testament prophets.
  
  Dale Tronrud has been discussing some of these issues for a long time;
  you might look at the following reference.
  
  TRONRUD, D. E. Knowledge-based B-factor restraints for the refinement of
  proteins. J. Appl. Cryst. 29, 100 (1996).
  
  If you are going to refine your B-factors much you really must use the
  bulk solvent correction and all of the low resolution data.  This has
  the added bonus of making your difference maps significantly clearer.
  
  Lynn Ten Eyck
  teneyckl@sdsc.edu
  

• In his review of volumes 276 and 277 of Methods in Enzymology, Jan Drenth (Structure 6, Feb 1998, pp. 243-4) writes: "The contributions of Alwyn Jones (and his co-authors) are extremely useful for the novice in model building and refinement practice. They are also a useful refreshment course for the experienced crystallographer, although the schoolmaster style of writing may irritate some readers"

• During the 1996 Summer School at the Karolinka Institute, Lennart Nilsson referred to us as "The Uppsala Structure Police".

• The best program never written by the Uppsala Software Factory has to be APRIL !

• In the IUCr Newsletter (vol. 6, nr. 2, p. 10), Mitch Guss writes about the meeting of the Society of Crystallographers in Australia (held in Queenstown, NZ, April 1997): "The relentless growth of protein crystallography in the region was heralded by the opening talk of G. Kleywegt who together with his Swedish colleague A. Jones has set out to inflict some of the accepted standards of small molecule crystallography onto the world of protein structure."

• In her review of volumes 276 and 277 of Methods in Enzymology, Elinor Adman (Acta Cryst D54, 709-710, 1998) writes: "The chapter on detecting folding motifs, by Kleywegt and Jones, describes tools for detecting similar folds, even during the process of map fitting, and includes good references to the larger community of structural consumers interested in classifying folds and detecting similarities." (but not a word about the other chapter ...)

• Way back in 1994, Laurence Pearl proposed to honour and immortalise Gerard's name as follows:

  
  From:   SMTP%"pearl@bsm.biochemistry.ucl.ac.uk"
  To:     "Members of CCP4BB mail list" 
  CC:
  Subj:   In Honour of Gerard K...................
  
  Resent-From: 
  Date: Thu, 25 Aug 1994 09:34:02 GMT
  Resent-Date: Thu, 25 Aug 94 10:35:51 UT
  Message-ID: <94825103551.~INN-ZQAa00165.ccp4bb@dl.ac.uk>
  
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                             HONOURING GERARD
  
  *******************************************************************************
  
  >From time to time you get a derivative that has a big loud isomorphous
  difference, and looks at first sight as though it should really solve the
  structure.
  
  However as time goes on it becomes clear that this big derivative will not
  deliver the phasing power it first promised, and in the end it contributes
  nothing to the final map except some irritating and unnecessary noise.........
  
  In keeping with the fine old crystallographic tradition of naming things 
  
  after people (Bijvoet, Friedel, Laue, Harker, Patterson etc.), I would like
  to propose that we honour our dear colleague Gerard (with whom it has so much
  in common), by naming this kind of derivative a 'Kleijwegt'.                    
  I do hope this nomenclature catches on ......
  
  
  Laurence Pearl
  
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