Uppsala Software News @ 2000-12-22
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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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       +-----------------------------------------------+
       | The final USF News of the second millennium ! |
       +-----------------------------------------------+


* LSQMAN Version 7.6
********
- New set of ALter commands to manipulate chain and segment IDs
  without having to go through MOLEMAN(2) (or to use sed or to
  edit PDB files)
- Speeded up the BRute_force command a little bit
- Implemented some commands to make it easier to use LSQMAN with
  nucleic acids:  ATom_types C4*, ATom_types NUcleic_acid_backbone,
  NUcleic_acid_pdb_nomenclature, SEt NUcleic_acid_defaults, and
  OMacro DEfine


* ODBMAN Version 1.9.5
********
- Removed nasty bug from ALl_corr command
- Changed dimensioning (max 100 ODBs of size 10000)
- New 3D_odl_file command to generate ODL file with spheres whose
  coordinates are taken from 3 datablocks (all scaled to range 0-100)


* SPASM Version 3.5
*******
- Fixed a bug in SPASM and MKSPAZ (from now on, the
  side-chain coordinates of alanine residues will be their
  CB coordinates rather than their CA coordinates ...)
- Various minor bug fixes and small improvements


* SAVANT Version 1.3
********
- Major bug fix (the output macro, when executed in O, would
  not put the hits on top of the pattern ...)
- Various minor bug fixes and small improvements


* XPLO2D Version 2.8.9
********
- Fixed a tiny wee little pico-buglet :-) [not in Linux version yet]


* Web sites
***********
- I have added Google and AltaVista search boxes to the search pages
  for both the Uppsala Software Factory and the HIC-Up site. This
  is actually in most cases the fastest way to find what you are
  looking for on these sites (if it's there and if the search
  engines' databases are up-to-date).


* DOMBO
*******
Volume 9, issue number 4 (12 December, 2000), 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


I won't be back in the lab until early January, 2001, a
space odyssey. Have a Merry Christmas (modulo local religious
belief system) and a Shagadelic New Millennium (modulo local
time-keeping convention) everybody !!!


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


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

PRAVITY: physical deformity ("no amount of make-up can help you
 defy the Law of P.")
PREANTEPENULTIMATE: the fourth from last ("please hand me the p.
 bottle from that shelf")
PREPUCE: foreskin ("the protein was painstakingly isolated from
 10,000 kilo of p.")
PROLEGOMENA: preliminary remarks; long introductions ("writing
 original p. to an article is quite difficult")
PROTEAN: infinitely variable ("there are indications that protein
 folds are not p.")
PSILOSOPHER: superficial philosopher ("... and someone who has
 limited knowledge of protein folds is a phi-psi-losopher")
PTARMIC: snot-promoting, sternutatory, errhine ("this protein
 causes the p. symptoms in allergic reactions")
PURPURACEOUS: purple, purpurescent ("the heavy-metal derivative
 had a deep p. colour")
PYGOPHILOUS: buttock-loving ("she's the living proof that fat is
 a p. substance")
PYRIFORM: pear-shaped ("p. women get pregnant more easily than
 apple-shaped ones, I read in the newspaper")
QUADRIGAMIST: someone who has married four times ("I say, is that
 fellow really a q. ?")
QUAESITUM: objective; true value ("the ultimate q. is to measure
 the q. of this quantity")
QUANTULUM: small quantity ("I always add a q. of BOG to my
 crystallisation solutions")
QUASIHEMIDEMISEMICENTURY: one 16th of a century ("a typical PhD
 takes a q.")
QUIDDITY: essence or nature of a thing ("once you've built your
 skeleton, you've uncovered the q. of your protein")
QUIRE: set of folded sheets fitting one within another; collection
 of 24 sheets of the same size ("the structure can best be described
 as a beta-q.")
RECLIVATE: sigmoid, S-shaped ("if we plot X versus Y, we obtain
 a r. curve")
RECREMENT: waste product, impurity; something secreted from the
 body, then reabsorbed ("saliva is the best example of a r., for
 most people anyway")
REDARGUTION: refutation ("if there doesn't exist a r. of a receptary
 (unproved fact; postulate), that doesn't mean it's true")
REDDITION: translation, explanation ("could you render a r. of this
 paragraph ?")
REPAND: having a wavy or undulating outline ("look how nicely r. my
 mask has turned out")
RETICULUM: network ("thanks to Castor the whole bloody r. is down
 again")
RETRAD: backward ("dummy, you've traced the whole chain r. !")
RETRORSE: bent backward or downward ("two of the sheets were r.")
RETROUSSE: turned up ("two of the sheets were r.")