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

[Objcryst-foxx] Fox 1.1.1 (bugfix version) & Call for Help

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

	Hi all,
 
   A new version of Fox is available, to fix unstabilities under windows 
(sorry about that ; the tests ran just before launching the new version did 
not show that).

FOX is a tool for the ab initio structure determination from powder 
diffraction (neutrons, X-Ray) and single crystal data (eg extracted 
intensities). The crystal structure can be described as any 
combination of atoms, molecules or polyhedras, without any assumption about 
the connectivity of these units. Fox can make multi-pattern global 
optimizations, and automatically correct special positions.

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/


*HELP NEEDED*
   Due to the recent problems with the 1.1 version under windows, I would 
very much like to have people testing new versions of Fox on a more regular 
basis during the developement. You do *not* need any programming skills for 
this. It would really be helpful, since I work only under Linux, and 
unfortunately windows is much less forgiving towards errors.
   What would be necessary for this is to install the (free) Borland 
compilers on a windows machine (win'98 and above), as well as the sources for 
wxwindows and Fox. You would then recompile regularly Fox, and run examples 
on it, to see if something has been broken under windows which I did not see 
under Linux.
   Do *not* be afraid about that recompiling: you just need to tape "make" in 
a DOS window and wait one minute for the new version of Fox to be compiled. 
And the update of Fox sourcefiles is just point mouse & click thanks to nifty 
cvs tools. I honestly think that after this has been done once, it shouldn't 
take more than 10 minutes each time you redo a test (and then you can leave 
Fox working as a test).

  Please contact me directly (mailto:vi...@us...) if you 
think you can help. Since I moved to the ESRF it is not my main project 
anymore so I have less time, especially for quality tests ! You can do this 
either if :
   * you believe Fox is a very useful tool and would like to help
   * would like to encourage free, open-source crystallographic software
   * want to have a say in future evolutions of the program
   * want to access/test the latest developements

   Of course testers under Linux are welcome, too !

#### 1.1.1 - 2002/01/17
BUG FIXES
   * Under windows, the global optimization lead to a crash after
     some random time.
   * Under windows, clicking on some part of a powder pattern graph 
     would make Fox crash

#### 1.1 - 2002/01/8
NEW FEATURES
   * Now it is possible to import Z-matrices to build a molecule 
     structure (eg a Z-matrix file can be generated from a .pdb file
     using babel, and then imported into Fox)
   * Added integrated R and RW factors as new cost functions (thus
     less sensitive to badly defined profiles). Unless you have *very*
     good profile parameters, I recommend using the integrated Rw as
     a cost function.
   * Now it is recommended to choose an "exponential" schedule for
     the amplitude, from 8 to .125, and a "smart" schedule for the
     temperature. This should be optimized for *all* experiments,
     so that users don't have to guess the right choices.
   * It is no longer necessary to validate all input by hitting the
     'return' key (which was *very* annoying)
   * Ability to zoom on the powder pattern graph, using the left button
     (double-click to unzoom)
   * Possibility to reduce the part of the displayed unit cell in 3D 
     view (use the popup menu with right-click)
   * Significant speed improvement.
   * The Parallel Tempering algorithm has been tuned to yield a higher
     success ratio.
   * Possibility to used single-crystal data (eg extracted intensities)
     for crystal structure optimization (honest crystallographer's note:
     if you have high quality extracted intensities, try direct methods
     first...)
   * Added interface for 2theta zero/displacement/transparency
     parameters in a Powder Pattern object
   * Added an overall temperature factor (Biso) for each crystalline 
     phase in powder diffraction (also available in single crystal).
   * new examples for organic molecules (potassium tartrate and 
     cimetidine with powder & extracted pseud-single crystal
     intensities)
   * The program now forbids to check lattice or profile parameters
     for a global optimization.

-LINUX:
   * Now using a distribution from source using the wxWindows RPM, which
   * should make things easier under Linux.

-BUG FIX:
   * under linux, the antibump cost function was not properly restored
	  from an xml file (preventing merging of identical atoms)
	* Changing the spacegroup (and thus extinction rules) will now
	  will re-generate the list of reflections for powder diffraction.
	  Same if the lattice parameters or the wavelength has changed.
   * a number of minor bugfixes...

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

[Objcryst-foxx] Fox 1.1.1 (BugFix)-Test Version

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

	Hi all,

     I have finally managed to correct the bug which made the last version of 
Fox (1.1) rather unstable under windows. I also corrected another bug which 
only occured under windows when clicking in some places of a powder pattern 
graph.

    A test version if available at:
   ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

    If you can test this one with the examples (especially PbSO4 and the 
cimetidine.xml ones with graph windows open) for more than 1 hour, it would 
be great.

    Sorry for all who endured the bugged version. This one should be much 
more stable. I will probably post the final 1.1.1 on thursday night or friday.

		Vincent

[Objcryst-foxx] FOX new version

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

	Hi all,

[Thanks to all who tested this new version this week. A few bugs have been 
removed, and the final release was updated yesterday]

FOX is a program for the ab initio structure determination from powder 
diffraction (neutrons, X-Ray). The crystal structure can be described as any 
combination of atoms, molecules or polyhedras, without any assumption about 
the connectivity of these units. Fox can make multi-pattern global 
optimizations, and automatically correct special positions.

Changes:

#### 1.1 - 2002/01/7
NEW FEATURES
   * Now it is possible to import Z-matrices to build a molecule 
     structure (eg a Z-matrix file can be generated from a .pdb file
     using babel, and then imported into Fox)
   * Added integrated R and RW factors as new cost functions (thus
     less sensitive to badly defined profiles). Unless you have *very*
     good profile parameters, I recommend using the integrated Rw as
     a cost function.
   * The Parallel Tempering algorithm has been tuned to yield a higher
     success ratio.
   * Now it is recommended to choose an "exponential" schedule for
     the amplitude, from 8 to .125, and a "smart" schedule for the
     temperature. This should be optimized for *all* experiments,
     so that users don't have to guess the right min and max
     temperatures.
   * It is no longer necessary to validate all input by hitting the
     'return' key (which was *very* annoying)
   * Ability to zoom on the powder pattern graph, using the left button
     (double-click to unzoom)
   * Possibility to reduce the part of the displayed unit cell in 3D 
     view (use the popup menu with right-click)
   * Significant speed improvement.
   * Possibility to used single-crystal data (eg extracted intensities)
     for crystal structure optimization (honest crystallographer's note:
     if you have high quality extracted intensities, try direct methods
     first...)
   * Added interface for 2theta zero/displacement/transparency
     parameters in a Powder Pattern object
   * Added an overall temperature factor (Biso) for each crystalline 
     phase in powder diffraction (also available in single crystal).
   * new examples for organic molecules (potassium tartrate and
     cimetidine with powder & extracted pseud-single crystal
     intensities)
   * The program now forbids to check lattice or profile parameters
      for a global optimization.
	  
-BUG FIX:
   * under linux, the antibump cost function was not properly restored
     from an xml file (preventing merging of identical atoms)
   * Changing the spacegroup (and thus extinction rules) will now
     will re-generate the list of reflections for powder diffraction.
     Same if the lattice parameters or the wavelength has changed.
   * a number of minor bugfixes...

-- 
Vincent Favre-Nicolin
ESRF- Grenoble, France
tel: +33 (0)4 76 88 27 27
http://v.favrenicolin.free.fr

[Objcryst-foxx] Test version of Fox available

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

	Hi all, and best wishes for this new year,

     A new version of Fox (1.1) is almost ready to go. Since I cannot fully 
test it especially under Windows, I have put a test version only available at:
	ftp://ftp.unige.ch/pub/soft/crystal/fox/test/

     This is only a test version, so do not spread this announcement. If 
everything is OK, I will make a release version (without debug messages) next 
tuesday or wednesday, unless there is something major wrong with this release.

     It would be nice if you could test this on different Windows versions (I 
only tested Windows NT4-SP4 under emulation). [I expect Win'95 (as well as 
NT4 ServPack1) still to crash when using the 3D crystal view]. Tell me if 
something goes seriously wrong, with the examples or any of your files 
(especially with the 3D view, or zooming in the powder pattern).

         Thanks

	Vincent

Changes:
#### 1.1 - 2002/01/7
NEW FEATURES
   * Now it is possible to import Z-matrices to build a molecule 
     structure (eg a Z-matrix file can be generated from a .pdb file
     using babel, and then imported into Fox). You still need to
     manually indicate free torsion bonds, though.
   * Added integrated R and RW factors as new cost functions (thus
     less sensitive to badly defined profiles). Unless you have *very*
     good profile parameters, I recommend using the integrated Rw as
     a cost function.
   * Now it is recommended to choose an "exponential" schedule for
     the amplitude, from 8 to .125, and a "smart" schedule for the
     temperature. This should be optimized for *all* experiments,
     so that users don't have to guess the right schedule nor the
     correct min and max values.
   * It is no longer necessary to validate all input by hitting the
     'return' key (which was *very* annoying)
   * Ability to zoom on the powder pattern graph, using the left button
     (double-click to unzoom)
   * Possibility to reduce the part of the displayed unit cell in 3D 
     view (use the popup menu with right-click)
   * Significant (I hope) speed improvement.
   * The Parallel Tempering algorithm has been tuned to yield a higher
     success ratio.
   * Possibility to used single-crystal data (eg extracted intensities)
     for crystal structure optimization (honest crystallographer's note:
     if you have high quality extracted intensities, try direct methods
     first...)
   * Added interface for 2theta zero/displacement/transparency
     parameters in a Powder Pattern object
   * Added an overall temperature factor (Biso) for each crystalline 
     phase in powder diffraction (also available in single crystal).
   * new examples for organic molecules (potassium tartrate and 
     cimetidine with powder or extracted pseudo-single crystal
     intensities)

-- 
Vincent Favre-Nicolin
http://v.favrenicolin.free.fr/

[Objcryst-foxx] Fox 1.01- Bug Fix

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

	Hi all,

     The version which was uploaded yesterday night had a bug which prevented 
profile FWHM less .06 degrees (.001 radians). This is fixed in the new 
version (1.01) available. Sorry for the mistake.

	Vincent

[Objcryst-foxx] New version of Fox available

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

	A new version of Fox "Free Objects for Crystallography" is
available. This new release fixes a few serious or annoying bugs,
and adds support for multiple phases in powder patterns. See
the full changelog at the bottom.

FOX is a program for the global optimization ( ab initio
structure determination) of crystal structures
(mainly) from powder diffraction patterns (neutrons, X-Ray).
Components of the crystal structure can be described as atoms,
molecules using a Z-Matrix description, or polyhedras.

Fox is available from sourceforge:
   http://objcryst.sourceforge.net
and from the CCP14 mirrors (mirroring should be done 
monday morning):

   (UK)     http://www.ccp14.ac.uk/ccp/web-mirrors/objcryst/
   (Canada) http://ccp14.sims.nrc.ca/ccp/web-mirrors/objcryst/


CHANGELOG-v 1.0
-NEW FEATURES
   * support for multiple crystalline phases in Powder Diffraction (you
      can optimize several "unknown" phases from one pattern ...
      provided you managed to index them...)
   * the Windows version now displays a console to give a better idea
     about what the program is doing.
   * Import of Sietronics data files (.cpi)
   * Linux binary version also available for glibc 2.1
   
-BUG FIXES:
   * removed another bug in ZMatrix interpretation, which prevented the  
     correct coordinates to be generated when using mono/triclinic unit
     cells (thanks Mark Edgar).
   * the program will no longer crash when importing data with null or 
     negative points.
   * U,V and W parameters leading to negative profile width will no
     longer crash the program (profile forced to be strictly positive)
   * various cosmetic bugs

and, for people who did not update from v0.9 to 0.9.1:
#### 0.9.1 Beta - 2001/09/20
-NEW FEATURES
   * Added menus to change limits globally in a ZScatterer(bond,angles)
   * Now the pivot atom (around which the ZScatterer is rotated, and
     which corresponds to the displayed x,y,z position of the 
     ZScatterer) is saved in the .xml file. It can also be changed 
     from a menu.
   * Limits can be changed individually for all parameters, using a 
     popu menu: right-click on the parameter name to get the local menu

-BUG FIXES:
   * removed a nasty bug in ZMatrix interpretation, which prevented  
     the correct coordinates to be generated  for chains longer than 3 
     atoms. Did not affect polyhedras... (thanks Yuri Andreev)


	peace,

	     Vincent Favre-Nicolin

[Objcryst-foxx] FOX Update

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

Due to a nasty bug when interpreting ZMatrices, a new version of FOX is 
out. It is only important to upgrade if (1) you want to create your own 
molecules using the ZScatterer approach, or (2) if you want to be able 
to change the refinable parameters limits.

CHANGELOG:

#### FOX 0.9.1 Beta - 2001/09/20
-BUG FIXES:
   * removed a nasty bug in ZMatrix interpretation, which prevented the
     correct coordinates to be generated  for chains longer than 3 
     atoms. Did not affect polyhedras... (thanks Yuri Andreev)

-NEW FEATURES
   * Added menus to change limits globally in a ZScatterer 
(bond,angle,dihedral)
   * Now the pivot atom (around which the ZScatterer is rotated, and
     which corresponds to the displayed x,y,z position of the
     ZScatterer) is saved in the .xml file. It can also be changed from 
     a menu.
   * Limits can be changed individually for all parameters, using a 
     popu menu: right-click on the parameter's name

-- 
Vincent Favre-Nicolin                http://www.unige.ch/crystal/favrev/
Laboratoire de Cristallographie      Phone: +41 (22) 702 60 79
24 quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland        Fax: +41 (22) 702 61 08

[Objcryst-foxx] First release of FOX-Global Optimization of crystal structures from powder diffraction

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

  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 free of charge in compiled form 
for Linux(x86) and windows (tested on 98 & NT).

  It features a full graphical interface, and allows the definition of 
crystal structures using atoms, polyhedras, or molecules using a 
Z-Matrix approach. Optimized for inorganic structures, it allows the 
automatic correction of special positions/ shared atoms via a 
'dynamical' correction of the occupancy of overlapping atoms.
  
  Available algorithms are Simulated Annealing and Parallel Tempering, 
using as a criterion the weighted sum of cost functions (R, Rw, 
anti-bump...). The ObjCryst++ library on which the program is based can 
be used to expand these algorithms and cost functions easily (a new 
version for this library will be available shorlty).
  
  FOX can also be used for education purposes: to display structure, 
simulate a powder diffraction pattern, see the influence of the 
structure/spacegroup,etc..


Information can be found on the FOX Home page:
   http://objcryst.sourceforge.net
and (once mirroring is done) on the CCP14 mirrors:
 (thursday morning):http://www.ccp14.ac.uk/ccp/web-mirrors/objcryst/
 (not yet working): http://ccp14.sims.nrc.ca/ccp/web-mirrors/objcryst/


   The FOX program was developped using the Object-Oriented 
Crystallographic Library (ObjCryst++), by Vincent FAVRE-NICOLIN, in 
collaboration with Radovan CERNY, at the University of Geneva.

This project is supported by the Swiss National Science Foundation.

-- 
Vincent Favre-Nicolin                http://www.unige.ch/crystal/favrev/
Laboratoire de Cristallographie      Phone: +41 (22) 702 60 79
24 quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland        Fax: +41 (22) 702 61 08