Uppsala Software News @ 981230
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                 http://xray.bmc.uu.se/usf/
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                  HAPPY NEW YEAR EVERYBODY !
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* OOPS Version 5.2
******
- New option to include WHAT IF diagnostics (read from a file called
  "pdbout.txt", that is generated by WHAT IF if the command:
           check ful filename.pdb x y
  is executed).


* LSQMAN Version 7.1
********
- Skip alternative conformations when reading PDB files.
- Error trap when no atoms are found in an input PDB file.
- Print histogram(s) for some of the plot commands (PHipsi, DIstance,
  DDihehral, and D1_D2).
- DIstance_plot now also includes residues from mol1 that were not
  found in mol2 (distance for those is plotted at a negative value).
- Print D-values after IMprove; after superimposing molecule I and J,
  D(I) = %Matched(I,J) * %SeqID(I,J) / 10000.  D(I) is a measure of how
  "easy" it should be to construct a homology model of I starting from J
  (sort of): D=1 means that I and J are identical in sequence and
  at least very, very similar in structure, whereas D=0 means there
  is no similarity between I and J in sequence and/or structure.
  (Still CASP-ing as you can see ...)
- New SImilarity_plot command to plot RMSD versus number of aligned
  residues.  This may be more informative than a single number when
  comparing two models.
- New CAsp command to assess RMS distances and number of matching
  residues between sequence-identical residues as a function of distance
  cut-off.


* DEJAVU Version 5.3
********
- Implemented "symbolic matching" where spatial arrangements of SSEs
  are not used, only their type and length (in terms of residues).
  This can be used if you get no hits at all, or if you have a *very*
  reliable secondary structure prediction.
- New SElect options to (de)select multiple entries.
- List total number of mismatched residues for every hit.
- List total number of gap-length differences (between neighbouring
  SSEs) for every hit.


* ESSENS
********
- Poul Nissen (Yale) has kindly contributed an ESSENS template for
  all RNA fans, a 5-basepair backbone fragment with which he has
  obtained good results.  The URL is:
    ftp://xray.bmc.uu.se/pub/gerard/rave/rave_doc/essens_rna5bp.pdb


* O2D Version 4.6
*****
- Add some comments to output PostScript files (in case you want to
  edit such files by hand).
- Don't hang on silly viewport (XMIN=XMAX or YMIN=YMAX).
- HIDE and NOHIDE keywords for 1D, scatter, pie, and histogram plots
  to white out everything outside the plot box (PostScript files only).
- CIRCLE and ELLIPS keywords for 1D, scatter, pie, and histogram plots.


* ODBMAN Version 1.9.1
********
- Minor bug fixes (REad and CGraph commands; makes that the SGI version
  actually works again ;-).


* VOIDOO Version 3.1.3
********
- Minor bug fix (bail out if no atoms accepted).


* FLOOD Version 1.1.1
*******
- Changed maximum mask size to 6 MWord.


* XPAND Version 1.3.1
*******
- Minor bug fix (if all atoms have identical coordinates, the program
  won't crash any longer ;-).


* DATAMAN Version 5.7.1
*********
- Add a few comments to output PostScript files.
- Print F/Sigma for systematic ABsences.
- Improved handling of orbital multiplicity and (a)centric flags.


* MOLEMAN2 Version 2.2.1
**********
- Add some comments to output PostScript files.


* SPASM
*******
Since DEJANA (part of DEJAVU) can now also handle O macros generated
by SPASM, this program is now also included in the SPASM distribution.
It can be used to sort the hits (and remove the poorest ones) from
an O macro generated by SPASM or DEJAVU.


* HIC-Up
********
- Some of the most popular hetero-compounds are now listed in the
  menu frame of the HIC-Up site under "QuickXS".
- A new way to locate a particular hetero-compound uses index
  lists of all compounds that contain the same set of elements
  (click on "Composition" in the menu frame).


* OMAC
******
Lots of small changes, and a couple of new entries.
- dirtar now prefers gzip (but will use compress if gzip is not
  installed).
- yasspa.omac & lefth.odb = updated version of the macro to colour
  your protein by secondary structure, now including left-handed
  helical fragments (defined in the file lefth.odb).
- transl_zone.omac = translate a zone of a molecule by a user-specified
  (Cartesian) vector in O.
- boxy.omac, cd.pdb & db.odl = macro etc. to delineate a part of 3D
  space (e.g., if you want to know where a blob of density is, such
  as your yet-to-be-traced molecule).  It draws a big box, made up
  of 8 water molecules.  By grabbing or moving atoms, you can make the
  box encompass your density.  Then sam_at_out your molecule, and read
  into MOLEMAN2 to get the (Cartesian or fractional) limits of this
  part of space.  For ease of use, also make sure that the OMAC classic
  baton_moving_atom.odb is in your local OMAC directory ;-)
- table_kind.dat = O property table to assign an integer number to
  every residue (1=Protein, 2=Nucleic acid, 3=Water, 0=Other).
- plt2mol.pl = a Perl script to convert a single Oplot object to
  Molscript 2.0 external object interface format, for getting maps
  from O into Molscript. (Contributed by Charlie Bond.)
- hetero_coord_gen.xplor = X-PLOR input file to generate coordinates
  (starting from *random* ones) for a hetero compound, using restraints
  from an appropriate topology and parameter file.


* ADDRESS
*********
From the first of January, 1999, we will become part of a brave
new institute.  Our address changes to: Department of Cell and
Molecular Biology, Uppsala University, Biomedical Centre, Box 590,
SE-751 24 UPPSALA, SWEDEN. (Only affects the Jones lab.)


--cd


CD's Words of the Month:

DAEDAL: ingenious, highly skilled, intricate and varied ("D-CUP
  is a d. little program")
DEFENESTRATE: throw out of a window ("you don't d. a computer just
  because the window manager d. you")
DEFOEDATION: pollution ("first, purify your protein to get rid of
  any d.")
DELENDA: things to be deleted ("the first draft of a manuscript
  usually turns out to be a collection of d.")
DELIQUESCE: to dissolve by absorbing moisture from the air
  ("unfortunately, the crystals d. after three days")
DELITISCENT: hidden ("if you type 'ls -al' you can see your d. files")
DELPHIC: ambiguous ("the results of their analysis are a trifle d.")
DEPHLEGMATE: to distil ("always d. your organic solvents before
  using them")
DEPREDICATE: to publish ("somehow he always managed to d. in the
  best journals")
DERODIDYMUS: two-headed monster ("to most people, a twinned crystal
  is like a d.")
DESECATE: to cut off ("we used a three-sigma criterion to d. our
  reflections")
DESPARPLE: to scatter ("the crystal didn't seem to want to d. the
  X-rays to any noticeable extent")
DESUETUDE: disuse ("FRODO is in a state of d. in our lab")
DEWDROPPER: one who sleeps by day and plays by night ("most of the
  computer enthusiasts in our lab are d.")