Uppsala Software News @ 2001-02-19
              **********************************

                  http://xray.bmc.uu.se/usf/
               ftp://xray.bmc.uu.se/pub/gerard/
             (ftp://molbftp.icm.uu.se/pub/gerard/)


* SPASM Version 3.7
*******
- New SPASM library files are available from the ftp server:
  - SPASM 25% October 2000 (1328 PDB entries; 5 MB compressed)
  - SPASM 95% October 2000 (5861 PDB entries; 22 MB compressed)
  - SPASM 100% January 2001 (7287 PDB entries; 34 MB compressed)
  The first two are based on the lists of Uwe Hobohm. The third
  contains all sequence-unique chains in the PDB. The latter is
  the recommended version. It contains roughly 1.8 million residues.
- Implemented a new substitution option in which the user may define
  for each individual residue by which residue type(s) it may be
  replaced.
- Implemented use of MAXHITS (to limit the total number of hits
  generated in case of "unfortunate" parameter settings), either
  as an environment variable or as a command-line argument (the
  default value is 1000)


* DEJAVU Version 5.7
********
- New DEJAVU library files are available from the ftp server:
  - DEJAVU 25% October 2000 (1339 PDB entries; 1 MB compressed)
  - DEJAVU 95% October 2000 (5888 PDB entries; 3 MB compressed)
  - DEJAVU 100% January 2001 (7348 PDB entries; 4 MB compressed)
  The first two are based on the lists of Uwe Hobohm. The third
  contains all sequence-unique chains in the PDB. The latter is
  the recommended version. It contains roughly 155,000 secondary
  structure elements.
- Increased dimensioning for new library files
- Implemented use of MAXHITS (to limit the total number of hits
  generated in case of "unfortunate" parameter settings), either
  as an environment variable or as a command-line argument (the
  default value is 1000)
- Expanded output from STats command


* RIGOR Version 2.4
*******
- New library file (January 2001) containing 21,076 motifs
  (generated automatically by an artificially stupid program,
  mind you ! caveat emptor !)
- New version of MAKRIG (2.3) with minor fixes
- Implemented use of MAXHITS (to limit the total number of hits
  generated in case of "unfortunate" parameter settings), either
  as an environment variable or as a command-line argument (the
  default value is 1000)


* DOMBO
*******
Volume 10, issue number 1 (5 February, 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
By the way - do you think that you've got what it takes to be
a DOG (Dombo Official Groupie) (R) (C) ? Go to the Dombo website
and find out !!!


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


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

SMARAGDINE: emerald-green ("why do you use that awful s. colour
  for contouring ?")
SMELLFUNGUS: grumbler, faultfinder ("every department needs a s.
  to critically read all manuscripts before they are submitted")
SNAFFLE: slight restraint ("have you tried refining the structure
  with NCS s. ?")
SNOD: trimmed; smooth ("what a cute s. mask you have on the screen
  there")
SOCKDOLAGER: something unusually large or imposing ("this protein
  is a veritable s.")
SODALITY: fellowship ("despite his s., he remained an affable chap")
SPELEOLOGIST / SPELUNKER: one who explores and studies caves ("with
  VOIDOO, anyone can be a protein s.")
SPERMOLOGER: seed gatherer ("if you want to isolate crambin, you'll
  have to become a s. first")
SPUTATIVE: apt to spit ("what's the difference between a putative
  scientist and a s. one ?")
SQUABASH: to crush by criticism ("his grossly exaggerated claims
  were s. immediately")
SQUIDGEREEN: a short, insignificant person ("I think 'vertically and
  intellectually disadvantaged' is the PC expression for a s.")
STEATOPYGIA: fatty-assedness ("no, that's s., not fatty-acidness !")
STERCORICOLOUS: living in dung ("do s. beetles send in a stercoriculum
  vitae when they apply for a job ?")
STULTILOQUENCE: silly talk, babble ("the speaker at the conference
  dinner had perfected the art of s.")
SUANT: smooth, even, regular ("try to make your molecular envelope s.")
SUAVILOQUENCE: bland or soothing, agreeable talk ("'cut the crap' is
  a dysphemism for 'spare me your s.'")
SUBBOREAL: cold, but not freezing ("you should grow those crystals in
  s. conditions")
SUBINGRESSION: a hidden entrance ("the van der Waals surface revealed
  a s. to the ligand cavity")
SUBTEGULANEOUS: indoor ("I'm glad that molecular biology is a s.
  branch of science")
SUI GENERIS: unique; in a class by itself ("this protein's fold is
  truly s.g.")
SUPERANNUATED: made obsolete; disqualified because of old age ("FRODO
  is a s. program, thanks to O")
SUPERCALIFRAGILISTICEXPIALIDOCIOUS: atoning for extreme and delicate
  beauty while highly educable ("the stunning student soon turned out
  to be s.")
SUPEREROGATORY: superfluous; non-essential ("this is going to Nature,
  so leave out all s. details such as Ramachandran plots")
SYMPHORIC: accident prone ("don't let that s. student handle any
  glassware !")