Uppsala Software News @ 2001-05-04
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                  http://xray.bmc.uu.se/usf/
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               ftp://xray.bmc.uu.se/pub/gerard/
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* LSQMAN Version 8.1
********
- New MPlot command to generate plots of the multiple-model-RMSD as a
  function of residue number (RMS distance of all unique pairs of
  corresponding residues in multiple chains or models).
- Increased dimensioning to allow for 120000 atoms
- NWunsch command to do a quick sequence-based alignment that
  can be applied to the structure (uses the BLOSUM-45
  substitution matrix)
- GLobal_nw command to do a global sequence alignment of two
  molecules, but based on the current structure alignment. So
  at last you can get your structure-based sequence alignments
  straight out of LSQMAN ! (See the manual for examples and
  details.)
- My current recipe for superimposing/aligning two structures
  "ab initio" (example uses ferredoxin and ubiquitin, allegedly
  a "difficult case"):
	=> read m1 pdb1fxi.ent
	=> read m2 pdb1ubq.ent
	=> brute m1 a m2 a 30 15 100
	=> improve m1 a* m2 a*
	=> show m1 m2
	=> global m1 a m2 a 5
	=> apply m1 m2
	=> write m2 1ubq_rt.pdb
  This yields (within seconds and with minimal effort):

	 Sequence 1 ASYKVTLKTPD-GDNVITVPD--D---EYILDVAEEEGLD---LPYSCRAGACSTCAGKL
	    |=ID           ||         |    |                                    
	 Sequence 2 --MQIFVKTLTGKTITLEV-EPSDTIE-NVKAKIQDKEGIPPD-Q----------QRLIF
    
	 Sequence 1 VSGPAPDEDQSFLDDDQIQAG-Y-ILTCV--AYPT----GD-CVIETH------KEEALY
	    |=ID                                                                
	 Sequence 2 --------------------AGKQLE--DGR-TLSDYNIQKESTLHLVLRLRGG------
    
	 Gap penalty         : (  12.500) 
	 Raw alignment score : ( -1.061E+03) 
	 Length sequence 1   : (      96) 
	 Length sequence 2   : (      76) 
	 Alignment length    : (     120) 
	 Nr of identities    : (       4) 
	 Perc identities     : (   5.263) 
	 Nr of matched res   : (      52) 
	 RMSD (A) for those  : (   1.864) 


* MAPMAN Version 7.2
********
- Implemented output format TURBO (DSN6 maps for Turbo-Frodo)
- Implemented input format MPI (for MPI-style EM maps)
- New SEt_value command (mostly for Mark's debugging exercise)


* O2D Version 5.3.1
********
- Implemented an option to produce box plots (useful if you
  want to see trends in large amounts of bin-able data; see
  e.g. Figures 2 and 3 in U Dengler, AS Siddiqui & GJ Barton,
  Proteins 42, 332-344 (2001))
- Minor bug fix (only affected the Alpha version)


* ODBMAN Version 2.1.3
********
- Minor increase in dimensioning (maximum datablock size 11000)
- Several minor changes and bug fixes


* ProSAL
********
- Added a couple of new services to ProSAL (Protein Sequence
  Analysis Launcher), such as GeneQuiz, MetaFam, RADAR, HCA
  and iProClass (http://xray.bmc.uu.se/sbnet/prosal.html)


* HIC-Up
********
- Updated HIC-Up. It now contains information on 3,078
  hetero compounds (http://xray.bmc.uu.se/hicup)


* OMAC
******
- A new "hetero.pdb" file, containing 3,078 compounds, is available


* DOMBO
*******
Volume 10, issue number 3 (25 April, 2001), is now available
from a Dombo web site near you:
       http://xray.bmc.uu.se/dombo
Contributions for Dombo can be sent to:
       mailto:dumbo@xray.bmc.uu.se?subject=copy


--DVD (The Crystallographer Formerly Known As "CD")


The Crystallographer Formerly Known As "CD"'s Words of the Month:

VEGA: a fertile meadow ("once he had solved three structures on it,
  he called his graphics workstation 'v.'")
VIBRATIUNCULATION: a slight vibration ("even a v. can disrupt your
  crystallisation trials")
VICISSITUDINARY: pertaining to mutation ("has anyone studied the v.
  effects on this protein's activity ?")
VRAISEMBLANCE: appearing to be true ("the v. of the Molecular
  Replacement solution was deceptive")
WHISKERINO: a beard-growing contest ("if you need hairs for seeding,
  just organise a w. among your male colleagues")
WITZELSUCHT: emotional state characterised by futile attempts at
  humour ("w. must be a German word")
WOOM: beaver fur ("did she use her w. for seeding ?")
XANTHOCHROID: having blond hair and a light complexion ("Sweden, home
  of the x.")
XANTHOCYANOPSIA: form of colour blindness in which only yellows and
  blues are seen ("most Swedish sports commentators seem to suffer
  from x.")
XERES: sherry ("if she had been Spanish, we would call her x.")
YCLEPT: called, named ("we describe a new program y. OOPS")
ZENZIZENZIZENZIC: the eighth power of a number ("no, no. no; it
  varies with the cube, NOT with the z., of the distance")
ZUGZWANG: in chess, when any move weakens the position ("... but z.
  is also when you have fear of flying so that you are forced to
  travel by train, like Dennis Bergkamp")
ZZXJOANW: a Maori drum ("the FINAL word in this series is z. !!!")