[Objcryst-foxx] Fox new version -1.5 (and a word about software patents in Europe)

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        Hi all,

   First of all remember that there will be a vote on the 1st of september =
in=20
the European Parliament on Software Patents. Allowing patents on algorithms=
=20
or any other parts (graphics,...) of a program would put a threat on small=
=20
development companies as well as scientists publishing free software, and=20
prevent many innovations. Please think about writing to your European=20
representatives (http://wwwdb.europarl.eu.int/ep5/owa/p_meps2.repartition) =
to=20
stop that. References:
http://www.iucr.org/iucr-top/comm/ccom/newsletters/2003jan/ (page 76)
http://swpat.ffii.org/
http://swpat.ffii.org/news/03/plen0626/index.en.html

   On to less important things, there is a new version of Fox available. [f=
or=20
those who got the beta versions from the university of Geneva, this is=20
version 1.5.0.3, previous versions had a few bugs].

  Most important changes are a new Molecule modelization using restraints,=
=20
more efficient for structure solution. This version is also much faster on=
=20
powder patterns, and the number of required trials has also diminished by a=
=20
factor 2 for the cimetidine and potassium tartrate examples. I hope it can =
be=20
used to solve more complex samples, especially organic ones.
   Many thanks go to Brian Toby for its help on the 3D display of crystal=20
structure & fourier maps, as well as polishing the CIF output function.

  Warning: if you use windows and have an Intel extreme graphics type card,=
=20
you must decrease the level of hardware acceleration so that there is no 3d=
=20
acceleration.

This version of Fox can be obtained:
ftp://ftp.unige.ch/pub/soft/crystal/fox/
http://sourceforge.net/project/showfiles.php?group_id=3D27546&release_id=3D=
167682
ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/
http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/
http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/
http://ccp14.minerals.csiro.au/ccp/ccp14/ftp-mirror/objcryst/

Changelog:
NEW FEATURES-MAJOR CHANGES
   * The optimization will now use log(likelihood) as a criterion:
     in practice, this means that the Chi^2 statistics are used
     rather than the user-chosen cost functions. The likelihood
     can sometimes be parametrized in the objects (crystal, pattern),
     but not any more in the Global Optimization objects.
   * Added a Molecule class, which supersedes the ZScatterer approach
     The scatterer is defined by a list of atoms, and restraints
     (bond lengths, angles and dihedral angles) to specify the
     geometry. This gives more flexibility, allows a better=20
     convergence and allows to correctly define cyclic molecules.
   * Added the ability to define a statistical positionnal error
     for atoms, which will be taken into account following Maximum
     Likelihood principles (ML field in ScatteringPowers), of course
     with a significant amount of approximations to be computationnaly
     friendly.
   * CIF output (with the help of Brian Toby).

OTHER NEW FEATURES
   * Faster computation when using integrated profiles for powder
     pattern objects
   * Error bars are now displayed on the Powder Pattern graphical=20
     display.
   * Further improvements of the Fourier maps display (mostly from
     Brian Toby)
   * A cursor can be displayed in the center of the 3D Crystal view,
     its coordinates are displayed at the bottom of the window, with
     the value of Fourier maps (if any)
   * Added atom labels in 3D Crystal view (right-click menu to
     deactivate)
   * In OpenGL view of a Crystal structure, shift-dragging with left
     mouse button now correctly changes the center of the view without
     changing the rotation center.
   * Changed lighting model in 3D Crystal view
   * Added the ability to save structure factors from a
     DiffractionSingleCrystal object, including detailed contributions
     from different elements (useful for anomalous diffraction
     experiments)
    =20
BUG FIXES
   * Fixed bug when exporting to a Fenske-Hall z-matrix, the 4th atom
     was always repeated twice
   * Overall ZScatterer occupancy is now correctly taken into account.
   * Auto-save of xml files will now use local time rather than gmt.

=2D-=20
Vincent Favre-Nicolin
Universit=E9 Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net