Uppsala Software News @ 970212
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* LSQMAN Version 5.1
********
Implemented a new BRute_force command.  This can be used to find an
alignment/operator for two molecules of which you know that they show
structural similarity, but you can't be bothered to figure out which
residues in one molecule correspond to which residues in the other.
This may happen, for instance, when you compare two proteins from
different organisms, mutants, a structural fragment (NMR domain ;-)
with an intact model (X-ray), two molecules which "accidentally" share
a common domain, etc.  The program doesn't use any fancy
tricks, just many brute force attempts to align bits of one molecule
with bits from the other.  For trivial cases, the operation takes
less than a second (e.g., P2 myelin versus cellular retinol-binding
protein; both 10-stranded beta-barrels).  In more challenging cases,
it may take a minute (e.g., cellular versus serum retinol-binding
protein; 10- versus 8-stranded beta-barrels).  Even a really tough
case (1AYH versus 1CEL) is handled correctly (in about half a minute).
So, if -like I- you are too lazy to do manual superpositioning, or
to figure out which residues match with which residues, give the
BRute_force command a try.  There's also a new O macro which enables
you to use this mechanism from within O (see OMAC news below) !
  Implemented new HEtero command which enables you to strip HETATMs
upon reading PDB files (the default is to keep HETATMs).
  Two terrible bugs in the MAlign command fixed (thanks to Tim Allison;
announced earlier on O-info).
  Fixed two more bugs in the DIstance and DDihedral plot commands,
so that these commands now also work correctly for macromolecules
other than proteins (see new example for DNA in the manual; thanks
to Armin Maeder).


* OMAC
******
New entries for the OMAC directory (the collection of public-
domain O macros, shell scripts, etc.  E-mail your contributions
to mailto:gerard@xray.bmc.uu.se):

- align2.omac -> O macro which runs LSQMAN in BRute_force mode
  as described above to superimpose any two protein chains,
  apply the best operator, read the molecule back into O and
  draw its CA trace

- paint_bfac.omac -> macro to colour ramp a molecule by temperature
  factor (contributed by Aaron Oakley)

- make_o_poly_ala.f -> Fortran program to generate O poly-Ala
  datablocks (contributed by Dirk Kostrewa)

- brute.awk -> for desperate molecular replacers; takes AMORE
  rot-fun solutions and expands each solution into 27 new ones
  with ALPHA, BETA, GAMMA offset by -2, 0 and +2 degrees

- rshow.csh -> use gnuplot to show R and Rfree from an X-PLOR
  run (contributed by Charlie Bond)

- rplot.csh -> use gnuplot to make PostScript plot of R and Rfree
  from an X-PLOR run (contributed by Charlie Bond)

- pdb2pdbo.sh -> script to handle double conformations O by splitting
  your PDB file into two copies (contributed by Thomas Schneider)


* OOPS Version 4.5.2
******
O macros produced by OOPS no longer include any On_off commands
(O 6.x does not really like them).


* DEJAVU Version 5.1
********
Moved a few search parameters which are rarely used to a separate
PAramaters command.


* MOLEMAN2 Version 1.1.3
**********
Minor bug fix ("SElect ?" would crash on Alphas; thanks to Peter Brick).
  The command to create a PIR file now only writes one-letter code for
residues for which at least one atom has been selected (thanks to
Jean-Michel Rondeau).


--cd

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