objcryst-foxx — Announcements about FOX, the 'Free Objects for Xtallography' program.

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

[Favre-Nicolin V. <vi...@us...>]

        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

[Objcryst-foxx] Fox 1.5.0.3 beta

[Favre-Nicolin V. <vi...@us...>]

	Hi,

   I've made a few last changes before official release. In this version:

* The lists of bond lengths, bond angles and dihedral angles restraints are=
=20
now displayed in separate windows, which can be opened using the "Formula"=
=20
menu. This makes it more friendly to people working with large molecules=20
(>100 atoms), which had to wait for a _long_ time (minutes) before being ab=
le=20
to open the graphical view.

* Added a menu (in "Formula") to rigidify the molecule by automatically add=
ing=20
(almost) all possible dihedral angles. By default Fox does not add dihedral=
=20
angles when importing from a Z-matrix, so this will be necessary for people=
=20
who want to work in quasi-rigid body mode. You can selectively remove the=20
dihedral angles afterwards (again using the "Formula" menu) if you want to=
=20
allow only a few specific free torsions.

* fixed bug reading an xml file when there is no data in the pattern
* fixed incorrect determination of free torsion bonds for short bonds (wind=
ows=20
only)
* Correctly recompute resonant (anomalous) scattering factors when the=20
wavelength has changed

available from:
ftp://ftp.unige.ch/pub/soft/crystal/fox

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

[Objcryst-foxx] Fox 1.5.0.2 beta

[Vincent Favre-N. <vi...@us...>]

	Hi,

   There was still a bug in the previous version, when trying to=20
display a powder pattern before adding a background or crystalline=20
phase (thanks Louise Robins for reporting this). This is fixed in the=20
new 1.5.0.2 version, available at:
ftp://ftp.unige.ch/pub/soft/crystal/fox

	Vincent
--=20
Vincent Favre-Nicolin
Universit=E9 Joseph Fourier & CEA Grenoble (France)
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox 1.5.0.1 beta

[Favre-Nicolin V. <vi...@us...>]

	Hi,

   A new beta is available, again from:
ftp://ftp.unige.ch/pub/soft/crystal/fox

  Fixes from the previous version are:
=2D remove problem with scrolling on windows when inserting new scatterers =
or=20
converting a ZScatterer to a Molecule
=2D avoid division by zero under windows in some circumstances
=2D correctly take into account when the max sin(theta)/lambda is changed
=2D fixes crashes when adding powder pattern components (background or=20
crystalline phase)

   If you have any problem, please send me an xml file to reproduce it.

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

[Objcryst-foxx] Fox v1.5, new (last) beta, winXP status

[Favre-Nicolin V. <vi...@us...>]

	Hi all,

   I've had a few more reports about winXP crashes with the 3D display in F=
ox.=20
It turns out that all those who reported problem (so far) use an "Intel=20
Extreme Graphics" video card. I've played a day with it on a borrowed lapto=
p,=20
and it turns out many other programs (including very simple ones) using=20
OpenGL crash with this card when 3D acceleration is turned on.
   The bottom line is that I now label this as a bug in the 3D video driver=
,=20
unless someone has the same problem with a different video card. The=20
workaround for this is to diminish hardware video acceleration, until=20
Direct3D acceleration is disabled. This can be done in the display properti=
es=20
(right-click on the desktop to access display properties and navigate to th=
e=20
advanced settings till you can chose the level of acceleration).

   Otherwise, I've uploaded a new beta version of Fox, which should be the=
=20
final 1.5 release. This version changes:
=2D avoid crash under windows when there are some points with null intensity
=2D automatic resizing of panels, for people working with really large=20
structure(s)
=2D the cimetidine example with extracted refection intensities has been up=
dated=20
with constant weights, so as to run in un-weighted mode (since the extracte=
d=20
intenisties in that file have uncorrect sigmes)

   The new beta can only be found from the Universit=E9 de Gen=E8ve:=20
ftp://ftp.unige.ch/pub/soft/crystal/fox

   There are a few things I'd like to add but it will have to wait for the=
=20
next (minor) release:
=2D Fox is very slow when updating the display of large structures (e.g. >1=
00=20
atoms in a Molecule), or converting them from Molecule to ZScatterer
=2D allowing the Molecule to have several levels of flexibility : (1)=20
rigid-body, (2) rigid-body with user-chosen free torsion, and (3) automatic=
=20
assignment of free torsion. Currently (3) is implemented, and I believe wor=
ks=20
relatively well, but it may not be best for large structures with few degre=
es=20
of freedom (you have to add a lot of restraints manually).

   Please tell me if you have any problem with these packages. I'll make th=
e=20
release in a few days.

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

[Objcryst-foxx] Fox v.1.5 Beta test 2 , 3D crystal view woes (Win XP specific ?)

[Favre-Nicolin V. <vi...@us...>]

	Hi all,

   There is a new test version for Fox. There was a crash reported when=20
displaying crystal structures in 3D under win$ XP.
   I don't have access to XP, so I need to know whether the problem is stil=
l=20
there, or even present on other OS. I have now changed the way I display te=
xt=20
in the 3D view.

   Even if you have little time, just open an example and the 3D view of th=
e=20
crystal, and report if it works with you, telling which is you OS.
   Please also tell me if you do _not_ see the atom labels.

pre-compiled windows binaries at:
ftp://ftp.unige.ch/pub/soft/crystal/fox/test
ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test
http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/
http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/

  Note that the Fox zip files include the examples, and you can run the .ex=
e=20
directly from the directory, asI removed the dependency with the glut=20
library.

  Also, under pressure the vote on software patents at the Euro Parl. has b=
een=20
pushed back to september, 1st.

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

[Objcryst-foxx] Fox v.1.5 Beta test

[Favre-Nicolin V. <vi...@us...>]

	Hi all,

   After spending a good day writing letters to european representatives (h=
ope=20
some of you did the same, hum ?), I have put the last touch to the next maj=
or=20
version of Fox.
   This version really needs serious testing before release, as there are a=
=20
number of major changes, as you can see below. I'd very much like to see=20
tested:
	- your xml files, to see if there is no problem switching to the new globa=
l=20
optimization algorithm
	- any organic sample, as this should be much better handled by the new=20
Molecule object. You can convert any ZScatterer to the new Molecule object=
=20
using the import/export menu of the ZScatterer object. This rellay needs=20
testing
	- and of course the supplied Fox examples for the new Molecule format (see=
=20
the file below)

  This version is roughly 50% faster on powder patterns, and the number of=
=20
trials has also diminished by a factor 2 for the cimetidine and potassium=20
tartrate examples. I hope it can be used to solve more complex samples,=20
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.

The beta version of Fox can be obtained:
=2D for people compiling it, by updating to the latest CVS and re-compiling.
=2D for people under windows and no compiler, get it from the usual places:
ftp://ftp.unige.ch/pub/soft/crystal/fox/test
ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test
http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/
http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/

  You should get the Fox-20030625CVS.zip, and put the .exe in the same=20
directory as your old Fox.exe.
  You can also get the updated examples in examples-molecule.zip.


  Note that the new documentation should appear by friday on the Fox websit=
e=20
(delay due to sourceforge), at http://objcryst.sf.net/Fox/

   Report to me any success or failure, I intend to do the official release=
=20
sometime next week if everything goes all right.

	Cheers,
		Vincent

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 suprsedes 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

[Objcryst-foxx] Free Crystallographic software and software patents - European Parliament

[Vincent Favre-N. <vi...@us...>]

	Hi all,

   This is a message specifically for the users of Fox from the=20
European Union. Please read on as this is important, for the future=20
availability of free/open-source software, for Crystallography and in=20
general.

THE ISSUE:
   Software patents have been illegal so far in Europe, but this is=20
about to change. Although patents in general are useful, they lead to=20
serious abuse in the computing/algorithm business because it gives=20
the ability to large corporations to patent _extremely_ trivial=20
ideas, which can then use it to sue independent developers (such as=20
myself) or from small corporations, without leaving them any chance=20
to defend themselves (do you have a lawyer at hand ?).

   If you are not aware of this issue, please read a short article=20
that I wrote for the first issue of the IUCr computin Commission=20
NewsLetter, in html:
http://www.fr.iucr.org/iucr-top/comm/ccom/newsletters/2003jan/html/index.=
html#vincent
or in pdf (5Mb), page 76:
http://www.fr.iucr.org/iucr-top/comm/ccom/newsletters/2003jan/iucrcompcom=
m_jan2003.pdf

   Also interesting is the official "Study" of the European Parliament=20
(longer). It clearly states that open-source developpers and small=20
and medium enterprises will be the victims of such a system ("study"=20
document at the bottom):
http://www.europarl.eu.int/hearings/20021107/juri/default_en.htm
Why he concludes that patents should be allowed just for the sake of=20
large companies, can be understood from the intense lobbying of large=20
US software corporations.


WHAT HAPPENS NOW:
   Oponents (basically everybody but large software corporations and=20
greedy lawyers) are slowly gaining ground (especially with the=20
increasing use of open-source software in governmental bodies), but=20
the text will be voted on ON THE 30TH OF JUNE, instead of the=20
previously scheduled date at the autumn. In a smart move they put it=20
on the first day of the session, in a 2hour session only, where few=20
representatives are likely to be there, and when no debate will=20
happen.

WHAT YOU CAN DO:
   Use your phone and pen&paper (email will _not_ be very efficient),=20
fax maybe, and write to your European representative. Explain them=20
the issue, that this would give almost aboslute power to large=20
corporations to decide which "free" software is allowed to exist.
   Is the distribution of software like Fox going to require having a=20
lawyer at hand ??

You can find the adress of the representatives at:
http://wwwdb.europarl.eu.int/ep5/owa/p_meps2.repartition?

NOTE: Such an issue is important. Taking half or even a full day for a=20
lifetime with the freedom to create and distribute freely _your_=20
program is really worth it.

	Regards,
		Vincent

PS: I will not apologize for the inconvenience to people in the list=20
who believe scientists should not meddle with politics, because they=20
are wrong. It actually is our duty.
--=20
Vincent Favre-Nicolin
Universit=E9 Joseph Fourier & CEA Grenoble (France)
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox v1.3 test version

[Vincent Favre-N. <vi...@us...>]

=09Happy new year !

   There's a new version of Fox upcoming. I put test versions before the=20
holidays (precompiled and source packages) in the usual 'test' directory:
ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

   It would be great if you had time to test these packages, and report a=
ny=20
success of failure with them. I'll make the new release next week if=20
everything goes OK.

   I did not want initially to make a new release before the next major=20
changes upcoming, but the serious spg bug required a fix...

Changelog
#### 1.3 - december 2002
NEW FEATURES
   * Added scattering power for a sphere, e.g. to modelize a
     disordered fullerene.
   * Added the option to use pseudo-crystallographic symmetry in a
     Crystal structure (i.e. use a spacegroup which is not allowed
     by the unit cell). Could be useful for phase transitions.
   * Added data format for FullProf formats 4 (synchrotron) and=20
     6 (multi-detector, LLB G42)
   * Now more than 100 atoms can be displayed in a ZScatterer unit.
   * Added the ability to set relative limits on all scatterer
     translations from their current positions.
   * Added the ability to run Fox without the graphical interface,
     once all objects to be optimized have been setup and saved in
     a xml file (see the reference part of the manual).
  =20
BUG FIXES
   * Fix serious bug in the dtermination of systematic extinctions,
     which lead to missing reflections for (body|face)-centered
     spacegroups with a center of symmetry not on the origin
     (e.g. for Fd3m (Si,...))
   * Fixed various bugs in the display and update of powder patterns

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

[Objcryst-foxx] Fox web page problem

[Vincent Favre-N. <vi...@us...>]

	Hi,

   Apparently there was a problem with the Fox Home page=20
(http://objcryst.sf.net/Fox/) during the last weeks. There was a css=20
file with a wrong name... Unfortunately, Linux browsers (mozilla,=20
konqueror) did not report any error and displayed the web page fine, so=20
it took me a while to see what was wrong. Now it should display OK - I=20
just tested with netscape & IE5 on a Mac-please tell me if there is=20
something wrong under windows.
   If you have a web cache locally, you may need to wait till the cache=20
has been updated. The CCP14 mirrors will be updated tomorrow morning as=20
usual.

   Thanks to those who reported this, and sorry for the delay, now=20
everybody (not just the privileged Linux users) should be able to see=20
the 'new' Fox pages (includes a link to the JAppl.Cryst. Fox article,=20
by the way).

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

[Objcryst-foxx] Fox 1.2 for windows update

[Vincent Favre-N. <vi...@us...>]

	Hi all,

   It appears there was a mistake in the august 9th release of Fox for=20
windows: the precompiled version packed was of august, 1st, and did not=20
include the new documentation, tutorials and examples (only the Fox=20
application without the glut32.dll...).
   You can now get the revised zip package from the usual places.

   Those using either the Linux or the source code for windows are not=20
concerned by this.

   And if you have remarks about the doc (missing parts, other FAQ=20
etc..), please tell me !

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

[Objcryst-foxx] FOX version 1.2

[Vincent Favre-N. <vi...@us...>]

	Hi,

  The FOX program ('Free Objects for Xtallography') is a program for 
the Global Optimization of Crystal Structures from powder diffraction 
data (X-Ray, neutron). It is available freely in compiled or source 
form for Linux and windows (tested on 98,NT,2000,XP).

   A new version of FOX "Free Objects fo Xtallography" is available. It 
adds the handling of preferred orientation, plus numerous bugfixes, 
especially under windows.

Fox is available from
   http://objcryst.sourceforge.net
and the CCP14 mirrors:
   http://www.ccp14.ac.uk/ccp/web-mirrors/objcryst/
   http://ccp14.semo.edu/ccp/web-mirrors/objcryst/
   http://ccp14.sims.nrc.ca/ccp/web-mirrors/objcryst/

   Note that you can compile Fox from the source code (on 
windows&Linux), which will enable you to have more 
frequent updates, and also help me (hint,hint)

   Thanks to all who helped or made suggestions for this release.

Changelog:
NEW FEATURES
   * FOX now supports Preferred Orientation, using the March-Dollase
     model. The texture parameters can be searched ab initio.
   * The 3D display of the crystal structure is now also refreshed
     automatically under WinNT and above (still much less responsive
     than under Linux -hint,hint).
   * The default size of crystal structure and powder pattern are more
     reasonable under windows.
   * New atoms in ZScatterer are now given a sensible default name,
     ScattPowName+number of the atom.
   * The wavelength is now directly displayed in the window, rather
     than exclusively through a menu.
   * Added ability to duplicate scatterers in Crystal.
   * Powder diffraction pattern keeps zoomed during optimization.
     
BUG FIXES
   * The atom names in ZScatterer are now validated without the
     'enter' key being hit.
   * Adding atoms in a z-matrix scatterer does not crash anymore.
   * removing a scatterer (or any object...) after running an 
     optimisation, does not crash any more when optimization is 
     relaunched (the parameter list is now correctly rebuilt).
   * Now correctly zooming when the dragged area goes beyond 
     2theta limits.


-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox v1.2 final, doc being updated

[Vincent Favre-N. <vi...@us...>]

	Hi,

   The Fox v1.2 is now ready to go. I have fixed several bugs thanks to 
reports & help from Lachlan. It is now in the CVS, and I have uploaded 
a new precompiled version at:
ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

    What is now lacking is the documentation, which is slowly improving. 
You can see the current state at:
http://objcryst.sourceforge.net/Goupil/
many parts are still missing, but if you want something in it, now's the 
time to ask for it. [I'll try to finish it tomorrow night, since I'm 
leaving on a short holiday on friday. I wonder whether it's better to 
wait for the documentation to be more complete to make a release -you 
tell me]

	Cheers,
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox v1.2 testing

[Vincent Favre-N. <vi...@us...>]

	Hi,

   I guess it's time to prepare for a new Fow release. I have fixed a 
nasty bug which was introduced 2 months ago and caused random crashes 
(especially under windows...). I also removed a bug when removing a 
scatterer an re-launching an optimization (thanks Lachlan for the 
report). Finally, the 3D crystal structure update during optimization 
should now work under win NT and above.
   Also, you will notice two new options in global optimization objects. 
The first is to save the evolution of all parameters during 
optimisation ; this is of course very slow and only for testing 
purposes, so don't select it (it won't be in the release, but if you 
want to have fun doing statistics on the evolution of parameters to see 
how the drunkard algorithm evolves...). The second is to save regularly 
the best configuration as a full xml file (every 10', 1h, 24h), in case 
you are making a very long run (did you use the sin(theta)/lambda limit 
to run faster ? Hmm??). The auto saved files are put in the directory 
where you launched Fox (in the Fox directory if you launched it from 
its icon).

   You can either update from the current CVS, or download a precompiled 
version from ftp://ftp.unige.ch/pub/soft/crystal/fox/test/. In the same 
directory there are two textured sample data (brucite & tartrate).

   There are two things I still have to work on before release, (i) the 
manual, and (ii) improving the convergence rate when searching texture 
parameters (for the tartrate, the correct solution is rarely found; 
even if the texture is extreme in that case it should be improved). If 
you have data with relatively strong preferred orientation and average 
complexity (something which is typically solved in about 100.00 moves, 
more than brucite), I'm looking for such data for tests !
   If you generated a xml file with the previous version and are using 
texture, I'd suggest right-clicking on the "March Coeff" name and 
reduce the limits to [0.1;10], which will be more reasonable and help 
in the search (it's the default now).

	Cheers,
		Vincent
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox with Preferred Orientation (again)

[Vincent Favre-N. <vi...@us...>]

	Hi all,

   I fixed the Preferred Orientation code in Fox, which should hopefully 
return better results now (although it still needs to be tested by 
people more experienced than me with texture, and compared with 
refinement results). As always you can update using the CVS for those 
who compile Fox from source, or you can grab a precompiled version for 
Windows in:
ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

   The ktartrate-textured xml file in the same directory has also been 
updated with new texture parameters (the texture is weaker than I 
previously thought, with "only" around 30% of the phase, but still a 
March parameter above 10).

   One thing which I still need to do is constrain the Preferred 
Orientation direction depending on the Crystal symmetry (e.g. in cubic 
structure, no direction to search, as it must be along any of the main 
axis, all 3 being equivalent).

   I also fixed the default size for 3D crystal structure and powder 
pattern, and now the 3D Crystal structure display should be 
automatically updated under WinNT and above.

   These are the most important features I want for the next FOX update 
(before the end of june normally), so if you have remarks on these, 
just drop me an email...

	Cheers,
		Vincent

PS: I also fixed the win makefiles for the unlucky ones using Win2K, so 
that the *first* compilation (or after a "make clean") should not stop 
after complaining  that it cannot find libCrystVector.lib. I don't have 
win2K here, so if you can 1) remove all the "bc32.mak" in the 
Fox\src\ObjCryst subdirectories 2) "cvs update" in Fox\src\objCryst 3) 
"make clean " then "make" (in Fox) and tell me how it goes, that would 
be great.
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] BUG in Preferred orientation

[Vincent Favre-N. <fa...@es...>]

=09Hi all,

   A bug has been found in the treatment of preferred orientation by Fox=20
(thanks Radovan !). The result is that the correction only if the symetry=
 is=20
at most orthorombic, *and* the preferred orientations are parallel to a m=
ajor=20
symetry axis... I'll correct that when I'm back from the ACA... May take =
some=20
time...

   Anyway I put a new version in=20
ftp://ftp.unige.ch/pub/soft/crystal/fox/test/, which is much faster than =
the=20
previous version (up to 2x), and with a number of bugfixes from version=20
1.1.2. The texture code is still wrong in that version, of course...

   Vincent
--=20
Vincent Favre-Nicolin
ESRF- Grenoble, France
tel: +33 (0)4 76 88 28 73
http://v.favrenicolin.free.fr
ObjCryst&Fox for Crystallography: http://objcryst.sf.net

[Objcryst-foxx] Fox with preferred orientation, corrected files

[Vincent Favre-N. <fa...@es...>]

=09Hi,

    I had put an old version of Fox on the server... I have corrected thi=
s=20
(also replaced the xml zipped file which had useless subdirectories). Sor=
ry=20
about that ! Bottom line: don't send files after midnight :-/
   as before, files can be found at:
ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

=09best,
--=20
Vincent Favre-Nicolin
ESRF- Grenoble, France
tel: +33 (0)4 76 88 28 73
http://v.favrenicolin.free.fr
ObjCryst&Fox for Crystallography: http://objcryst.sf.net

[Objcryst-foxx] Fox with preferred orientation

[Vincent Favre-N. <vi...@us...>]

	Hi all,

   Here are some new features to be tested in Fox: I have just added 
preferrred orientation (using the March-Dollase model). It shows a new 
menu at the bottom of each crystalline phase of Powder pattern objects 
(I'd advise using only one preferred orientation, that should be 
sufficient for structure solution purposes).
   You can obtain this either by using the CVS for those who can compile 
Fox themselves. Otherwise I have added a test version at :
ftp://ftp.unige.ch/pub/soft/crystal/fox/test/
  You will need to unzip the Fox application and put it in place of the 
one that you already have (to have the glut.dll file in the same dir). 
You may also want to take the ktartrate-textured xml file which is in 
the same directory. It includes data with a very strong preferred 
orientation (99%, March parameter>10), which makes it a good example 
but hard to find (Fox succeeds in about 30% of runs in less than 4 
hours on my 1.4 GHz).

   To be done : test this version of Fox (especially preferred 
orientation, *most* especially under windows...), and check that the 
texture parameters obtained are OK...
   I've fixed some bugs, too (like the one which prevented adding atoms 
in a ZScatterer by hand and not through a zmatrix).

   Hopefully after this I will do some improvements on the modelization 
of molecular compounds, and for their input into Fox which is not very 
user-friendly at the moment.

   Note that at the end of next week I'll be at the ACA in San Antonio. 
I will by presenting Fox in the powder workshop on the 25th, at 1:30 
PM. See http://www.chem.tamu.edu/xray/acaworkshop/

	Cheers,
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox for Powder v1.1.2 release... & a word about software patents

[Vincent Favre-N. <vi...@us...>]

	Hi all,

   Before going on, I would like that all of you take some time to 
think about the consequences of Software Patents if these are also 
enforced in Europe (they would then be legal more or less worldwide)... 
I've put a few words about this *major* issue on the main 
ObjCryst++/Fox web page. It would be a good thing if the 
scientific community (not negligeable postdocs like me...) was more 
active about this, to compensate the fact that only large corporations 
are being heard in the European Commission so far (the BSA, which is 
essentially a subsidiary of Microsoft, wrote the European draft on 
software patents...)

Note that if software patents are enforced in Europe, I may not be in 
a position secure enough (from the legal point of view) to distribute 
Fox any more.

***************
    There is a new version of Fox, which adds a few features (limit in 
sin(theta)/lambda, inhibit some parameters optimization..) and fixes a 
few bugs (when changing spacegroup/cell parameters, when importing 
z-matrices). An *experimental* option for twinned single crystal data 
is also included.

  The FOX program ('Free Objects for Xtallography') is a program for 
the Global Optimization of Crystal Structures from powder diffraction 
data (X-Ray, neutron). It is available freely in compiled or source 
form for Linux and windows (tested on 98,NT,2000,XP).

Fox is available from
   http://objcryst.sourceforge.net
and the CCP14 mirrors:
   http://www.ccp14.ac.uk/ccp/web-mirrors/objcryst/
   http://ccp14.semo.edu/ccp/web-mirrors/objcryst/
   http://ccp14.sims.nrc.ca/ccp/web-mirrors/objcryst/

   Note that you can compile Fox from the source code (on 
windows&Linux), which will enable you to help me, and have more 
frequent updates. For example, there already is the ability to display 
the enantiomer structure in 3d, but only in the development tree (hint, 
hint).

    Many thanks to those who are already helping!

Changelog:
#### 1.1.2 - 2002/02/18
License changed to the GNU General Public License.
NEW FEATURES
   * Added a maximum value of sin(theta)/lambda for diffraction
     data objects. All data above is ignored.
   * Added an *experimental* option in single crystal data for
     twinned data, to work on the sum of metrically-equivalent
     reflections. Entirely untested (contact me to use it !)
   * Some parameter are automatically fixed for global optimizations
     (unit cell, background & profile parameters).
   * Fox will write a few messages for some key events
     (importing data, creating spacegroup,...)

BUG FIXES
   * The dynamical occupancy correction now begins for interatomic
     distances below 1A, and proceeds to full correction for .1A
     (before that 2 and .8A where used (why?))
   * Spacegroup and Unit Cell values can now be changed even if
     scattering data has already been computed, without crash.
   * Importing a Z-Matrix would give the 3rd and 4th atoms the same
     number, and if atoms were of the same type, both atoms would
     have the same name in the .xml saved file, and would crash
     on reloading. Molecules thus created need to be re-imported.


-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] new test version of Fox 1.1.2 (Dyn Occup Correction mistake)

[Vincent Favre-N. <vi...@us...>]

	Hi all,

    Just saw this afternoon that the dynamical occupancy correction 
used wrong threshold values (2 Angstroems to begin correction, .8 to 
fully merge atoms). Changed this to normal values (1 and .1 
Angstroems), and updated the CVS. This would give wrong corrections for 
all compounds with bond distances below 2 A.

    So there is a new test version, at:

ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

    If you can test the windows (.zip) version for obvious bugs, and 
tell me if it goes fine or not, before the official release (postponed 
to next week).

	Cheers,
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Test version for Fox 1.1.2

[Vincent Favre-N. <vi...@us...>]

	Hi all,

    First, I would like to thank those among you who have downloaded 
the source and compiled Fox. It has proven slightly more difficult than 
expected (especially with the woes of the wxWindows setup.h files for 
2.2.9), but now the instructions should be OK. I hope that by updating 
more regularly from the CVS tree between realses, there will be more 
feedback and therefore less bugs, especially under windows. (btw, last 
small changes in CVS were made yesterday)

    I have put a new version of Fox (1.1.2, precompiled for windows), 
which is available from:
ftp.unige.ch/soft/pub/crystal/Fox/test/

   This new version will fix-I hope- most annoying bugs (zmatrix faulty 
input, changing spacegroup/unitCell +recomputing crash), and will also 
introduce a few useful features such as introducing a limit in the 
extent of calculations in sin(theta)/lambda, and an *experimental* 
option for twinned single crystal data (contact me for this, as I have 
made absolutely no test on it !).
   I hope to bring more major changes in the next version, ideally 
texture and a new modelization for molecules.

   On an aside note, the license has been changed to the GNU GPL, in 
order to bring more protection to the source code while still keeping 
it free (see http://www.gnu.org/philosophy/philosophy.html).
   Note that if some people want to use ObjCryst++ without being forced 
to reveal their own source code, it will still be possible by asking me 
directly, and it will be granted depending on the mode of distribution 
of the program (freely available being the idea).

    Cheers,

Changelog:
#### 1.1.2 - 2002/02/18
License changed to the GNU General Public License.
NEW FEATURES
   * Added a maximum value of sin(theta)/lambda for diffraction
     data objects. All data above is ignored.
   * Added an *experimental* option in single crystal data for
     twinned data, to work on the sum of metrically-equivalent
     reflections. Entirely untested (contact me to use it !)
	* Some parameter are automatically fixed for global optimizations
	  (unit cell, background & profile parameters).
   * Fox will write a few messages for some key events
     (importing data, creating spacegroup,...)

BUG FIXES
   * Spacegroup and Unit Cell values can now be changed even if
     scattering data has already been computed, without crash.
   * Importing a Z-Matrix would give the 3rd and 4th atoms the same
	  number, and if atoms were of the same type, both atoms would
	  have the same name in the .xml saved file, and would crash
     on reloading. Molecules thus created need to be re-imported.

-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox compile on Windows update

[Vincent Favre-N. <vi...@us...>]

	Hi all,

    Just solved another bug in the source distribution of Fox (Windows 
only), submitted by Lachlan Cranswick. Symptom: crashes when opening 
the 3D structure view (for example on cimetidine-powder).
    Cause: the glut32.lib was out of sync with the glut32.dll file. All 
you have to do is get the glut.h and glut32.lib file from:
   ftp://ftp.unige.ch/pub/soft/crystal/fox/tmp/

  and put the glut.h in Borland\Bcc55\Include\gl
  and the glut32.lib in Borland\Bcc55\Lib
(they should replace the old versions)

I will update the source package for Windows later today.

    *Please*tell*me* if you succedeed or not compiling Fox, so that I 
know if there is a problem. I'm thinking about doing a new release 
(1.1.2) to add a few features and fix a few bugs, so I need testing 
reports !

    Also tell me if you have succeeded or not in updating the source 
code using CVS, as I have little experience with cvs under windows 
(people behind firewalls may be unable to use anonymous cvs, but I need 
to know it !).

    Here are the last modifications in the CVS, compared to the last 
release:
    *added a max sin(theta)/lambda field to avoid high-angle data in 
the global optimization (generally sin(theta)/lambda < 0.25-0.35 should 
be sufficient)
    * For single crystal data, added a "twinning" option to work on the 
sum of metrically-equivalent reflections (when there is an unknown 
twinning). Warning: it's not tested at all so far !

    * fix a numbering of atoms bug when importing from a z-matrix, 
which in some cases would lead to a crash when re-loading froman xml 
file
    * fix a bug, which would lead to a crash when changing the lattice 
parameters when diffraction calculations have already been made on that 
structure.
    * more parameters will automatically be fixed when beginning a 
global optimization (background parameters, etc...)

	Cheers,
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] Fox compiling... last change

[Vincent Favre-N. <vi...@us...>]

	Hi all,

    A last modification is needed with the instructions I gave (thanks to 
Lachlan for being the first to endure this !)

   *Before* compiling wxWindows, you need to set:

#define wxUSE_DEBUG_CONTEXT 0

   in the wxWindows\include\setup.h file

   After that, it should (finally) work. (You will need to recompile 
wxWindows)

   Please tell me if you have any further problems.
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
tel: +33 (0)4 76 88 27 27 
http://v.favrenicolin.free.fr

[Objcryst-foxx] Re: Problems compiling FOX on Win98 - Fox source available !

[Vincent Favre-N. <fa...@es...>]

	Hi,

> C:\dev\fox>make
> MAKE Version 5.2  Copyright (c) 1987, 2000 Borland
>         cd src/ObjCryst/wxCryst
>         MAKE -f bc32.mak all
> MAKE Version 5.2  Copyright (c) 1987, 2000 Borland
>         MAKE -f bc32.mak lib
> MAKE Version 5.2  Copyright (c) 1987, 2000 Borland
>         bcc32  -c sgglobal.c
> Borland C++ 5.5.1 for Win32 Copyright (c) 1993, 2000 Borland
> sgglobal.c:
> Error E2209 sgglobal.c 7: Unable to open include file 'stdio.h'
> Error E2209 sgglobal.c 8: Unable to open include file 'stdlib.h'
> Error E2209 sgglobal.c 9: Unable to open include file 'string.h'

   My mistake... I did the configuration a too long time ago... The bcc32.cfg 
and ilink32.cfg must go in the Borland\BCC55\BIN directory (and not 
Borland\Bcc55)... (I had a copy in \Borland, one in \Borland\Bcc55 and one in 
Borland\BCC55\BIN !!)

	Vincent

[Objcryst-foxx] Fox source available !

[Vincent Favre-N. <vi...@us...>]

	Hello all Fox cubs !

    As announced last week, I have prepared a package with the Fox source 
code for windows (which was already available for Linux). I have also put 
instructions on how to compile Fox under windows using the Borland compiler, 
at the usual places:

   http://objcryst.sourceforge.net/
and the mirrors:

   http://www.ccp14.ac.uk/ccp/web-mirrors/objcryst/
   http://ccp14.semo.edu/ccp/web-mirrors/objcryst/
   http://ccp14.sims.nrc.ca/ccp/web-mirrors/objcryst/

   Go in the Fox home page and use the link on the left to see the directions 
to compile Fox. For windows users, it may not be very easy the first time but 
after it should be really easy and quick.

   Of course, do not hesitate if there is any problem with the compiling, or 
the instructions themselves, or getting the (free) borland compiler.

   Note that I have added all the people who volunteered to test Fox to the 
objcryst-foxx mailing list. If you do not wish to be on the list, just tell 
me and I'll remove you. But it is the only convenient way for me to reach 
everybody (I will not post development news to other lists). There are very 
few messages on this list anyway (ie my announcements).

   Note that in the lastest development version, which you will get if you 
manage to compile Fox (hint, hint), a few things have been fixed: increased 
crystal structure window, correctly update the fixed status of some buttons, 
disable global un-fixing of powder parameters.

	Cheers,

PS: once you got to testing the cvs, please tell me if you are behind a 
firewall who refuses cvs traffic (like at the ESRF).
-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net