Uppsala Software News @ 19991022
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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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* OMAC
******
New acquisitions in the OMAC collection of public domain scripts etc.:
- merge_cavities.csh: script to merge multiple cavities found by
  VOIDOO into one map file
- rsr_cns_oops.csh (from Carsten Schubert): extract real-space
  R-values from CNS into an O-style datablock for use with OOPS(2)
- ftp_hits: script to ftp the PDB files of "hits" found by SPASM if
  these are not available locally
- make_epmr_omac.csh: generate an O macro to read and display any or
  all EPMR molecular replacement solutions, including their symmetry
  mates
- sse2odl.f: a program to generate an ODL file with solid arrows from
  a DEJAVU SSE file
- uniquefy_objects.csh: script to uniquefy object names in a SPASM or
  SAVANT O macro
- plot_qs_progress.csh: plot progress of a Qs ("Queen of Spades") run


* SAVANT Version 1.0.1
********
- Implemented alternative residues/atoms for fuzzy pattern matching
  (e.g., when your Arg may also be a Lys, your Phe may also be a
  Tyr, etc.). NOTE: for this to work properly, you should also get
  a new version of the "savant.lib" library file !
- NOTE: with this version of SAVANT, the major drawback of SPASM
  (very fast searches, but not very sensitive) has been remedied.
  The results you can now get with SPASM/SAVANT/DEJANA are really
  very impressive (IMHO) ! See the examples in the SPASM tutorial:
        http://xray.bmc.uu.se/usf/spasm_tut.html


* SPASM Version 3.3.4
*******
- Implemented a cut-off for the maximum number of residues to enable
  the user to skip very big proteins
- For those of you who have noticed that searches for main-chain-only
  motifs take forever, this is caused by two rogue NMR entries in
  the SPASM database (1BM4 and 1BY0). You can either remove these
  from your copy of the SPASM database, or download an updated
  version from the ftp-server:
      ftp://xray.bmc.uu.se/pub/gerard/spasm/spasm_etc.tar.Z
  or use a resolution cut-off of less than 99 A so as to skip all
  NMR entries in your searches.
  (NOTE: the problem with 1BM4 and 1BY0 is that they do not
  contain MODEL ... ENDMDL cards to demarcate the various models.
  Since the N copies of the molecule are all roughly in the
  same place, the SPASM algorithm quickly gets stuck in a
  combinatorial explosion of biblical proportions ... I have
  notified the PDB :-)
- Expanded the SPASM tutorial (on the USF web site)
- Also note the new "ftp_hits" script in the OMAC directory (see above)


* DEJANA Version 1.4
********
- New option to toggle how the hits are sorted: either by number
  of matches first, and then by RMSD, or vice versa


* DATAMAN Version 5.8.1
*********
- New EO_plot command to detect subtle spacegroup errors in special
  cases (after: E. Carredano, PhD thesis, Uppsala, 1999)
- The RAmp_odl command finally works properly (i.e., it actually
  colour-ramps ...)


* MOLEMAN2 Version 2.4.1
**********
- New VRml CRamp_selection, SPhere, CYlinder, and LIquorice commands
- Debugged some of the VRML-generating routines
- D-amino acids are now explicitly handled in the Ramachandran plot
  (PRotein MC command). Their -Phi and -Psi values are used to assess
  if they are outliers, and they are shown as red diamonds in the
  PostScript plots


* O2D Version 5.0.2
*****
- Implemented LINFIT keyword for 1D line and scatter plots to
  calculate and draw the least-squares line through the data
  (assuming unit weights)


* LSQMAN Version 7.1.5
********
- Minor changes.


* ODBMAN Version 1.9.4
********
- Minor changes.


* ODBM Version 1.3.1
******
- Minor changes.


* LINUX
*******
I should be getting a little Linux portable soon, so I can (finally)
port the USF programs ...


* DOMBO
*******
Volume 8, issue number 7, is now available from the Dombo Journal
web site at: http://xray.bmc.uu.se/dombo


--cd


CD's Words of the Month:

GNOMONICS: the science of dial construction ("before using "O", take
  a course in g.")
GOOGOL: ten to the power 100 ("Molecular Dynamics on the millisecond
  time-scale still takes a g. hours of CPU-time")
GUNNEL: a small, slimy elongate marine blenny found on both sides of
  the Atlantic ("the protein was isolated from 60 kilos of g.")
GUTTATIM: drop by drop ("she examined her tray g.")
GYNOTIKOLOBOMASSOPHILE: one who likes to nibble on a woman's earlobe
  ("since the professor was a g., none of the women in his lab ever
  said that they were all ear")
HABNAB: at random; hit or miss ("his h. mutations haven't been very
  successful")
HADEHARIA: constant use of the word "hell" ("is sanguohadeharia the
  constant use of the expression "bloody hell" then ?")
HALOID: saltlike ("we obtained small h. crystals")
HARENGIFORM: herring-shaped ("why are my sill-y crystals h. ?")
HERMENEUTICS: the study of interpretation ("O is a program for
  electronodensitohermeneutics")
HETEROCLITE: irregular, unorthodox, abnormal ("the h. crystallisation
  conditions gave rise to h. crystals")
HOLOCRYPTIC: incapable of being deciphered without a key ("Unix Fortran
  compilers tend to give h. error messages")
HWYL: an emotional outburst of eloquence ("the Welsh professor claimed
  that he had re-invented the h.")
HYPERBOREAN: northern; any Arctic peoples ("no, h. doesn't mean that
  they're extremely boring")
HYPERMNESIA: unusually sharp memory ("Erling cut his finger while
  replacing some of the Alpha's h.")