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[sdpd] Fox new version -1.5 (and a word about software patents in Europe)
Hi all,
First of all remember that there will be a vote on the 1st of september in
the European Parliament on Software Patents. Allowing patents on algorithms
or any other parts (graphics,...) of a program would put a threat on small
development companies as well as scientists publishing free software, and
prevent many innovations. Please think about writing to your European
representatives (http://wwwdb.europarl.eu.int/ep5/owa/p_meps2.repartition) to
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. [for
those who got the beta versions from the university of Geneva, this is
version 1.5.0.3, previous versions had a few bugs].
Most important changes are a new Molecule modelization using restraints,
more efficient for structure solution. This version is also much faster on
powder patterns, and the number of required trials has also diminished by a
factor 2 for the cimetidine and potassium tartrate examples. I hope it can be
used to solve more complex samples, especially organic ones.
Many thanks go to Brian Toby for its help on the 3D display of crystal
structure & fourier maps, as well as polishing the CIF output function.
Warning: if you use windows and have an Intel extreme graphics type card,
you must decrease the level of hardware acceleration so that there is no 3d
acceleration.
This version of Fox can be obtained:
ftp://ftp.unige.ch/pub/soft/crystal/fox/
http://sourceforge.net/project/showfiles.php?group_id=27546&release_id=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
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
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)
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.
--
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net
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