Uppsala Software News @ 2000-12-01
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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 7.4
********
- Changed the default CA-CA distance cut-off from 3.8 A to
  3.5 A (you can still change it with the SEt DIst command,
  of course)
- Added optional "first residue" and "last residue" parameters to
  the WRite command, so you can selectively write a stretch of
  residues
- Did the same for the APply_operator command, so you can apply
  an operator to a stretch of residues
- Added the JUdge and CAsp commands to the menu (used during CASP3
  evaluation)
- New PErturb_operator command (to see how stable an operator is)
- Added an optional "cutoff" parameter to the commands MDihedral,
  MRamachandran, MSide, MTors, VMain, VSide and MBfactors so you
  can list only the residues whose NCS-mates show the largest spread
  in torsion angles, circular variance, or B-factors
- Some of the above changes were suggested by Thierry Fischmann


* MAPMAN Version 6.0
********
- New set of VRml commands enabling you to produce dot and
  contour drawings of your maps
- Increased dimensioning of arrays used in skeletonisation
- New WHere_value command to locate specific density values (within
  a certain tolerance) in your map


* MOLEMAN2 Version 2.8.1
**********
- PDb FArout command to generate quick-n-dirty HELIX and SHEET
  records for use with Dennis Madsen's program FarOut
  (see: http://xray.bmc.uu.se/dennis/manual/ for more info)
- NUcleic DUarte_pyle command to make "Ramachandran-like" plots to
  help analyse the conformation of RNA and DNA (see CM Duarte & AM
  Pyle (1998), J. Mol. Biol. 284, 1465-1478)
- New VRml CLose_file command


* STRUPRO Version 1.4
*********
- Much better profile parameters (should be more sensitive)
- Use flexible indel penalty


* MSEQPRO Version 1.3
*********
- Much better profile parameters (should be more sensitive)
- Use flexible indel penalty


* DATAMAN Version 5.8.5
*********
- Fixed a bug in the HKl_aniso_plot command (now it won't coredump
  when encountering Miller indices greater than 100 or less than
  -100 ...)
- Allow multipliers 2, 3, 4, 5 and 6 in CHange_index command
  (e.g., if you want to replace K by H+2K etc.)


* MAMA Version 5.6.2
******
- New VRml CLose_file command
- Minor bug fix


* O2D Version 5.2
*****
- Implemented XYSTAT keyword for 1D plots to calculate and print
  some statistics for the X and Y values as well as their RMSD and
  correlation coefficient


* XPLO2D Version 2.8.8
********
- AUTODIC option: increased maximum number of dihedrals (e.g.,
  needed for large cluster compounds)


* OOPS2 Version 1.1.1
*******
- Add non-breaking space to HTML table entries in case there
  are no error/warning messages


* ZPROF Version 1.1
*******
- Increased max nr of sequences from 100,000 to 1,000,000


* RAVE
******
Increased maximum number of NCS operators to 180 (upon request).


* OMAC
******
- New version of the "hetero.pdb" file, now containing 2640
  hetero compounds (up from 2290).


* HIC-Up
********
- HIC-Up, the Hetero-compound Information Centre - Uppsala,
  was updated in July and now contains information on 2,640
  hetero-entities that have been taken from the PDB (up
  from 2,290 in November, 1999).
  The URL for HIC-Up is:  http://xray.bmc.uu.se/hicup


* O Party !!
************
O is such a popular program in Munich that they even organised
a little party in its honour (even though Alwyn left there more
than two decades ago) ! See:
    http://xray.bmc.uu.se/usf/about.html
Thanks to Alexandru Tudor Constantinescu for submitting these
pictures.


* DOMBO
*******
Volume 9, issue number 3 (November 2000), is now available from
the Dombo web site at:
       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:

PECCATOPHOBIA: fear of sinning ("I'm sure that if you get to
  know Irmi a bit better, your p. will disappear")
PERENDINATE: to postpone until the next day, or indefinitely
  ("did you make those figures yet ?" - "errr, no, but I promise
  that I'll p. it today !")
PERICHAREIA: excessive and violent rejoicing ("prizes, foreign
  visitors, anything is an excuse for p. in this department")
PERIEGESIS: description of an area ("the p. of the dimer interface
  needs some more work")
PERJINKITIES: niceties ("you should describe the p. of the active
  site in a bit more detail")
PERVULGATE: publish ("p. or perish")
PHILALETHIST: truth-lover ("a philalethist-philatelist is an expert
  on fake stamps")
PHOBOPHOBIA: fear of phobias or fear of fear itself ("I don't like
  people who pretend to suffer from p.; does that make me a
  pseudophobophobiacophobe ?")
PHTHARTIC: deadly, destructive ("the Finnish custom of running naked
  through the snow after a sauna, is a potentially arctic p. habit")
PILLIWINKS: old instrument of torture for the thumbs and fingers
  ("the SGI dialbox is a modern version of the p.")
PLEXIFORM: complicated ("their paper is a bit too p. for me")
PLICATE: folded like a fan ("the protein is p.")
PLUMBEOUS: leaden; dull, heavy, stupid ("I used a p. compound for
  my p.-atom derivative")
PNEUMONOULTRAMICROSCOPICSILICO-VOLCANOKONIOSIS: pneumoconiosis caused
  by the inhalation of silicate or quartz dust ("our studies might
  eventually lead to a cure for p.")
POCULIFORM: cup-shaped ("the protein has a peculiar p. active site")
PODOBROMHIDROSIS: smelly feet ("this structure offers new insight
  into the molecular basis of p.")
POLYCHRESTIC: useful for many reasons ("if anything, MoleMan is a p.
  program")
POLYMICRIAN: compact ("all Alphas have a built-in p. disc player")
PONOPHOBIA: fear of overworking ("I've heard of p. but this is
  ridiculous")