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

[Objcryst-foxx] Fox @ IUCr Software Fayre Tuesday 12:00 in Hyderabad

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

		Dear all,

	For those of you in Hyderabad, I’ll be giving a Fox presentation tomorrow at the IUCr 2017 congress Software Fayre, at 12:00. 

	This will be the occasion to demonstrate possibilities in Fox, including some new features in the last version of Fox, available from:

		https://github.com/vincefn/objcryst/releases <https://github.com/vincefn/objcryst/releases>

	Best wishes,
		Vincent
-- 
Vincent Favre-Nicolin

Co-editor, J. Synchrotron Radiation http://journals.iucr.org/s/ <http://journals.iucr.org/s/>
Director, HERCULES school http://hercules-school.eu <http://hercules-school.eu/>
ESRF-The European Synchrotronhttp://www.esrf.eu <http://www.esrf.eu/>
71, Avenue des Martyrs
Grenoble, France

X-Ray NanoProbe (XNP) group

Tel: +33 4 76 88 28 11

On leave from Univ. Grenoble Alpes

Re: [Objcryst-foxx] Fox version 2016.2

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

		Dear all,

	A new (pre-release) version of Fox is available from:

https://github.com/vincefn/objcryst/releases/tag/v2016.2 

(see bottom of page for binaries for MacOS, Windows and Linux)

	This new version fixes a few issues found with the last release. Again, please send me any observation you have with steps to reproduce.

	Upgrade is strongly advised.

	List of changes is below.

		Best wishes,
			Vincent

#### 2016.2 (13 November 2016)
IMPROVEMENTS
  * faded atoms which are part of a Molecule which is centered in the display region
    are displayed with their names (if displaying names is activated).
  * CIF import: more informative messages when loading diffraction data
  * CIF import: better recognition of Molecules with higher coordination centers (Li,..),
                accept more polyhedra

BUG FIXES
  * correctly save optically active/non-flip atom status in .xmlgz files
  * correct bug in Le Bail mode/profile fitting which could lead to a crash
  


#### 2016.1 (6 November 2016)
NEW FEATURES
  * direct search on the Crystallography Open Database:
    - search using keywords, formula or lattice parameters
    - double-click to display the Crystal structure
    (this requires access to the default database port, 3306. Some firewalls
    may prevent that)
  * automatically recognizing Molecules and isolated polyhedra from CIF files
  * ability to combine several powder diffraction data sets from different 
    temperatures (or any other variable condition) to solve a single crystal 
    structure (it is possible to override the lattice parameters in 
    the powder pattern diffraction)
  * the extension for .xml.gz files is now .xmlgz
  * define 'optically active atoms' than will no be flipped during global (Jan Rohlicek)
    optimization (previously this was only possible using dihedral restraints)
  * support for anisotropic pseudo-Voigt profiles
  * support for ellipsoid texture description (Alexandr Zaloga)

IMPROVEMENTS
  * faster, more robust CIF import
  * better flexibility search for Molecules
  * 3D display: 
    - nicer using transparency (can be disabled from preferences)
    - standard atom colors from jmol
  * drag & drop files on MacOSX
  * take into account excluded regions when searching for peaks.
  * faster initial optimization (and randomization) of Molecules
  * Unicode interface (should be more friendly to directories with accents, symbols..)
  * localized number display (using , rather than . for decimal separation)
  
BUG FIXES
  * Avoid crashes during profile fitting and indexing
  * internal fixes (Pavol Juhas)

— 
Vincent Favre-Nicolin

Co-editor, J. Synchrotron Radiation  http://journals.iucr.org/s/ <http://journals.iucr.org/s/>

Director, HERCULES school   http://hercules-school.eu <http://hercules-school.eu/>

ESRF-The European Synchrotron    http://www.esrf.eu <http://www.esrf.eu/>
71, Avenue des Martyrs
Grenoble, France

X-Ray NanoProbe (XNP) group
Tel: +33 4 76 88 28 11

On leave from Univ. Grenoble Alpes

[Objcryst-foxx] Fox version 2016.1

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

		Dear all,

	A new (pre-release) version of Fox is available from:

https://github.com/vincefn/objcryst/releases/tag/v2016.1
(see bottom of page for binaries for MacOS, Windows and Linux)

	This new version focus should be faster and more stable, but I would appreciate if you send me some feedback in case you find an issue (with steps to reproduce).

	Full Changelog:
#### 2016.1 (November 2016)
NEW FEATURES
  * direct search on the Crystallography Open Database:
    - search using keywords, formula or lattice parameters
    - double-click to display the Crystal structure
    (this requires access to the default database port, 3306. Some firewalls
    may prevent that)
  * automatically recognizing Molecules and isolated polyhedra from CIF files
  * ability to combine several powder diffraction data sets from different 
    temperatures (or any other variable condition) to solve a single crystal 
    structure (it is possible to override the lattice parameters in 
    the powder pattern diffraction)
  * the extension for .xml.gz files is now .xmlgz
  * define 'optically active atoms' than will no be flipped during global (Jan Rohlicek)
    optimization (previously this was only possible using dihedral restraints)
  * support for anisotropic pseudo-Voigt profiles
  * support for ellipsoid texture description (Alexandr Zaloga)

IMPROVEMENTS
  * faster, more robust CIF import
  * better flexibility search for Molecules
  * 3D display: 
    - nicer using transparency (can be disabled from preferences)
    - standard atom colors from jmol
  * drag & drop files on MacOSX
  * take into account excluded regions when searching for peaks.
  * faster initial optimization (and randomization) of Molecules
  * Unicode interface (should be more friendly to directories with accents, symbols..)
  * localized number display (using , rather than . for decimal separation)
  
BUG FIXES
  * Avoid crashes during profile fitting and indexing
  * internal fixes (Pavol Juhas)

		Best wishes,
			Vincent
— 
Vincent Favre-Nicolin

Co-editor, J. Synchrotron Radiation  http://journals.iucr.org/s/ <http://journals.iucr.org/s/>

Director, HERCULES school   http://hercules-school.eu <http://hercules-school.eu/>

ESRF-The European Synchrotron    http://www.esrf.eu <http://www.esrf.eu/>
71, Avenue des Martyrs
Grenoble, France

X-Ray NanoProbe (XNP) group
Tel: +33 4 76 88 28 11

On leave from Univ. Grenoble Alpes

Re: [Objcryst-foxx] News for FOX, ECM29

[Vincent Favre-N. <vin...@uj...>]

	Dear all,

    I sent the wrong (private) link for the beta version. You can get it at:
https://cloud.vincefn.net/index.php/s/w6zyL0NGzGs6NMU <https://cloud.vincefn.net/index.php/s/w6zyL0NGzGs6NMU>
(the https certificate is self-signed so your browser will probably warn you)

    For Robert: this version also allows to hide/show hydrogens in the 3D crystal view (use the right-click popup-menu).

		Best,
			Vincent

> Le 25 août 2015 à 14:29, Vincent Favre-Nicolin <vin...@uj...> a écrit :
> 
> 		Dear all,
> 
> 	It has been a long time since the last news about Fox !
> 
> 	There have been few changes these last few years but a number of changes have been introduced these last few months, for a future Fox version. This will include:
> - automatically recognizing Molecules and isolated polyhedra from CIF files
> - more robust CIF import
> - direct search on the Crystallography open Database (search and then double-click to display the file)
> - ability to combine several powder diffraction data sets from different temperatures (or any other variable condition) to solve a single crystal structure (it is possible to override the lattice parameters in the powder pattern diffraction
> - better flexibility search for Molecules
> - 3D display: nicer using transparency, standard atom colors from jmol
> - drag & drop files on MacOSX
> - the extension for .xml.gz files is now .xmlz
> 
> 	This is still a beta version, but you can try a pre-release compiled version (windows and MacOSX) from:
> https://cloud.vincefn.net/index.php/apps/files/?dir=%2FFox
> 
> 	Also, you may know that part of the Fox/ObjCryst++ code was interfaced in the python language by Pavol Juhas/Chris Farro/Simon/Billinge to use the crystal structure description in the DiffPy project. A few days ago I added the ability to access diffraction objects and optimization 
> Played around with it and it should soon be also possible to run Fox-type optimization from Python scripts (see for example ‘powder.py’ in https://github.com/vincefn/CrystCompSchool/tree/master/pyObjCryst).
> 
> 	I am also at ECM29 if you have questions (I was too late to ask for a slot at the sofware Fayre).

-- 
Vincent Favre-Nicolin

Co-editor, J. Synchrotron Radiation http://journals.iucr.org/s/ <http://journals.iucr.org/s/>

Director, HERCULES school 		 http://hercules-schoool.eu <http://hercules-schoool.eu/>

Institut Nanosciences & Cryogénie	 http://inac.cea.fr <http://inac.cea.fr/>
CEA Grenoble             
Laboratoire SP2M/Nano-structures et Rayonnement Synchrotron
17, rue des Martyrs
38054 Grenoble Cedex 9 - France

Université Joseph Fourier        http://www.ujf-grenoble.fr <http://www.ujf-grenoble.fr/>

tél: (+33) 4 38 78 95 40           fax: (+33) 4 38 78 51 38

Re: [Objcryst-foxx] News for FOX, ECM29

[Vincent Favre-N. <vin...@uj...>]

	Dear all,

   I forgot to mention that the Fox/ObjCryst++ source code is now using GIT (the subversion repository is obsolete). You can follow it from:
https://sourceforge.net/p/objcryst/git/ci/master/tree/
or
https://github.com/vincefn/objcryst

	Best wishes,
			Vincent


> Le 25 août 2015 à 14:29, Vincent Favre-Nicolin <Vin...@uj...> a écrit :
> 
> 		Dear all,
> 
> 	It has been a long time since the last news about Fox !
> 
> 	There have been few changes these last few years but a number of changes have been introduced these last few months, for a future Fox version. This will include:
> - automatically recognizing Molecules and isolated polyhedra from CIF files
> - more robust CIF import
> - direct search on the Crystallography open Database (search and then double-click to display the file)
> - ability to combine several powder diffraction data sets from different temperatures (or any other variable condition) to solve a single crystal structure (it is possible to override the lattice parameters in the powder pattern diffraction
> - better flexibility search for Molecules
> - 3D display: nicer using transparency, standard atom colors from jmol
> - drag & drop files on MacOSX
> - the extension for .xml.gz files is now .xmlz
> 
> 	This is still a beta version, but you can try a pre-release compiled version (windows and MacOSX) from:
> https://cloud.vincefn.net/index.php/apps/files/?dir=%2FFox
> 
> 	Also, you may know that part of the Fox/ObjCryst++ code was interfaced in the python language by Pavol Juhas/Chris Farro/Simon/Billinge to use the crystal structure description in the DiffPy project. A few days ago I added the ability to access diffraction objects and optimization 
> Played around with it and it should soon be also possible to run Fox-type optimization from Python scripts (see for example ‘powder.py’ in https://github.com/vincefn/CrystCompSchool/tree/master/pyObjCryst).
> 
> 	I am also at ECM29 if you have questions (I was too late to ask for a slot at the sofware Fayre).
> 

-- 
Vincent Favre-Nicolin                    http://inac.cea.fr

Co-editor, J. Synchrotron Radiation http://journals.iucr.org/s/

Director, HERCULES school http://hercules-school.eu

CEA/Grenoble              Institut Nanosciences & Cryogénie
Laboratoire SP2M/Nano-structures et Rayonnement Synchrotron
17, rue des Martyrs
38054 Grenoble Cedex 9 - France

Université Joseph Fourier        http://www.ujf-grenoble.fr

tél: (+33) 4 38 78 95 40           fax: (+33) 4 38 78 51 38

[Objcryst-foxx] News for FOX, ECM29

[Vincent Favre-N. <vin...@uj...>]

		Dear all,

	It has been a long time since the last news about Fox !

	There have been few changes these last few years but a number of changes have been introduced these last few months, for a future Fox version. This will include:
- automatically recognizing Molecules and isolated polyhedra from CIF files
- more robust CIF import
- direct search on the Crystallography open Database (search and then double-click to display the file)
- ability to combine several powder diffraction data sets from different temperatures (or any other variable condition) to solve a single crystal structure (it is possible to override the lattice parameters in the powder pattern diffraction
- better flexibility search for Molecules
- 3D display: nicer using transparency, standard atom colors from jmol
- drag & drop files on MacOSX
- the extension for .xml.gz files is now .xmlz

	This is still a beta version, but you can try a pre-release compiled version (windows and MacOSX) from:
https://cloud.vincefn.net/index.php/apps/files/?dir=%2FFox

	Also, you may know that part of the Fox/ObjCryst++ code was interfaced in the python language by Pavol Juhas/Chris Farro/Simon/Billinge to use the crystal structure description in the DiffPy project. A few days ago I added the ability to access diffraction objects and optimization 
 Played around with it and it should soon be also possible to run Fox-type optimization from Python scripts (see for example ‘powder.py’ in https://github.com/vincefn/CrystCompSchool/tree/master/pyObjCryst).

	I am also at ECM29 if you have questions (I was too late to ask for a slot at the sofware Fayre).

		Cheers,
			Vincent
-- 
Vincent Favre-Nicolin                    http://inac.cea.fr

Co-editor, J. Synchrotron Radiation http://journals.iucr.org/s/

Director, HERCULES school http://hercules-school.eu

CEA/Grenoble              Institut Nanosciences & Cryogénie
Laboratoire SP2M/Nano-structures et Rayonnement Synchrotron
17, rue des Martyrs
38054 Grenoble Cedex 9 - France

Université Joseph Fourier        http://www.ujf-grenoble.fr

tél: (+33) 4 38 78 95 40           fax: (+33) 4 38 78 51 38

[Objcryst-foxx] Fox @ EPDIC

[Vincent Favre-N. <vin...@ce...>]

		Dear all,

	You may have seen there has been very little Fox development during the last year, as I’ve been busy on other subjects - and Fox is reasonably stable at this stage (many changes would be desirable but would probably require at lot of time and a profound rewrite). There were a few changes in the code in 2013 to improve the structure solution of large molecules including flexible cycles, although I did not release new precompiled versions of Fox.

	This being said, don’t hesitate to query me if you have a specific problem - I’m always happy to help or see what Fox is being used for.

	I’ll be present in Aarhus for EPDIC 2014 - and Radovan will also be there - so although I won’t talk about Fox don’t hesitate to query us if you have any question !

		Best regards,
			Vincent
-- 
Vincent Favre-Nicolin                    http://inac.cea.fr

Co-editor, J. Synchrotron Radiation http://journals.iucr.org/s/

CEA/Grenoble              Institut Nanosciences & Cryogénie
Laboratoire SP2M/Nano-structures et Rayonnement Synchrotron
17, rue des Martyrs
38054 Grenoble Cedex 9 - France

Université Joseph Fourier        http://www.ujf-grenoble.fr

tél: (+33) 4 38 78 95 40           fax: (+33) 4 38 78 51 38

[Objcryst-foxx] Fox at IUCr congress in Madrid

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

	Dear all,

   I will be later this week at the IUCr computing school in Oviedo, and
after that at the IUCr congress in Madrid.

   There will be a Fox demonstration (with Radovan Cerny & me) during
the Software Fayre - for Fox it is scheduled on Saturday (27th) at
15:30. Of course don't hesitate to drop me an email if you want to
discuss during the congress !

   Also, I have not sent announcement emails, but there have been  new
versions of Fox, see:
	http://vincefn.net/Fox/Changelog


	Vincent

[Objcryst-foxx] Fox 1.9 is available !

[Vincent Favre-N. <vin...@ce...>]

       Dear all,

  A new version of Fox is available ! Among the most important changes:
- rigid groups of atoms will now be kept rigid during least squares optimisation
- triclinic indexing now works

   You can download the new version from:

http://objcryst.sourceforge.net/Fox/Download

   The full Changelog is available at http://vincefn.net/Fox/Changelog
- the last changes are listed below.

   As always, please report any issue with this new version.

      Vincent

#### 1.9.0.1 - November 2009 (Revision #1204)
NEW FEATURES
  * Add automatic least-squares refinement of the structure during a
global optimization run
  * Take into account rigid groups during least-squares refinement
  * Working triclinic indexing
  * Allow manual adding of peaks for indexing without a peak search
  * Add manual least-squares refinement of the structure in the global
optimization run/stop menu
  * Better import of CIF files, using either the Hall symbol or the
symmetry_equiv_pos_as_xyz fields to avoid ambiguous space group
  * Enable auto-generation of powder patterns from a CIF file for both
X-ray and neutron radiation
  * When importing powder pattern CIF files, recognize both
_pd_proc_2theta_range_XXX and _pd_meas_2theta_range_XXX

BUG FIXES
  * Avoid deadlock (freezing fox) when using the 3D crystal view or
the powder pattern graph
  * Correct molecule rotation quaternion when using least squares
  * Correct log(likelihood) calculation using integrated intensities
(could cause invalid Chi^2 values when used without gui)
  * Correct Fullprof export when 3 or more independent atoms are overlapping
  * Work around visual c++ compilation bug during Fullprof export,
that would output U U U instead of U V  W parameters
  * Updated cctbx (and boost) version - fixes compilation with gcc 4.4
  * Enable importing Fenske-Hall zmatrices file both for human-written
files (with whitespace between fields), and for strictly formatted
files (sometimes without any space between fields)
  * Avoid giving up when encountering parameters with the same name,
notably for least squares refinements

-- 
Vincent Favre-Nicolin   -   http://vincefn.net
Université Joseph Fourier  -  http://physique-eea.ujf-grenoble.fr/
ObjCryst/Fox : http://objcryst.sf.net

[Objcryst-foxx] Beta version of Fox, with automatic least-squares refinement

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

       Hi,

   There is a new Beta version of Fox available - it features a new
automatic least-squares refinement during and/or at the end of global
optimization runs. This results (according to systematic tests) in an
overall 2x-5x reduction of the time needed to find the structure
solutions, particularly for flexible molecules.

   Note that this can lead to intermediate distorted structures, so
make sure to read the updated manual:
http://vincefn.net/Fox/Manual/Algorithm#options

   To get be new beta version, you must manually select the file (the
default file for Linux/windows/MacOSX is still the 1.8.2 version), so
you should go to:
https://sourceforge.net/project/showfiles.php?group_id=27546

   Please report any issue for this new version !

          Vincent

Changelog:
#### 1.8.X (Beta version) - April 2009 (Revision #1143)
NEW FEATURES
   * Add automatic least-squares refinement of the structure during
    a global optimization run
   * Add manual least-squares refinement of the structure in the
   global optimization run/stop menu

BUG FIXES
   * Correct log(likelihood) calculation using integrated intensities
   (could cause invalid Chi^2 values when used without gui)


-- 
Vincent Favre-Nicolin http://vincefn.net
Université Joseph Fourier http://www.ujf-grenoble.fr
ObjCryst & Fox: http://objcryst.sourceforge.net

[Objcryst-foxx] Fox 1.8.1 is available !

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

[It seems the first messages did not go through - apologies if you get
this in duplicate]

    Hi,

 A new release of Fox is available ! Everybody should upgrade, as this
 version fixes a few notable issues with the 1.8.0.x versions:

1) a speed problem when optimising powder patterns (5x speed slowdown !)
 2) under windows: a very slow read of uncompressed xml files
 3) under linux: various issues due to input/output in Fox unicode version

 Download the new Fox from:
 http://sourceforge.net/project/platformdownload.php?group_id=27546

 Please report any issue with this new version !

     Vincent

PS: here is the Changelog (full version @: http://vincefn.net/Fox/Changelog):

#### 1.8.1.2 - April 2009 (Revision #1117)
 BUG FIXES
 * Fix auto-scrolling bug with wxWidgets >=2.8.8
 * Better formatting of some fields (overall cost,...)

#### 1.8.1 - March 2009 (Revision #1113)
 NEW FEATURES
 * Add an option to use molecular dynamics random moves
 when generating new molecule conformations, for molecules
 with severe restraints (e.g. macro-cycles)
 * Add a menu to test random moves of a crystal structure for 30s

BUG FIXES
 * Correct calculation speed for powder patterns when using
 integrated profiles
 * Correct display of colours in 3D view for Mac OSX
 * Correct import of gsas raw format
 * Faster read of uncompressed xml files under windows
 * Many fixes for the Linux unicode build of Fox


--
Vincent Favre-Nicolin
Université Joseph Fourier http://www.ujf-grenoble.fr
ObjCryst & Fox: http://objcryst.sourceforge.net

[Objcryst-foxx] Fox update [1.8.0.3, revision 1088] for Linux (unicode fixes)

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

	Hi,

   This is only for Linux users: 

  There is an update for Fox, for all linux users using the 'unicode' version 
of Fox (i.e. compiled using unicode=1). The bug prevented the correct reading 
and writing of xml and cif files from the graphical interface, and the 
correct display of reflection labels, only when using unicode.

  To update, you can either:
1) go into the top "Fox" directory (not the Fox/Fox sub-directory), and 
do 'svn update' (you need subversion to be installed for this)

2) download the new version from the usual place:
http://sourceforge.net/project/platformdownload.php?group_id=27546

	Vincent
-- 
Vincent Favre-Nicolin

CEA Grenoble/INAC/SP2M			http://inac.cea.fr
Univ. Joseph Fourier (Grenoble) http://www.ujf-grenoble.fr

ObjCryst & Fox			http://objcryst.sf.net/Fox

[Objcryst-foxx] Fox 1.8.0 is available !

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

	Hi,

   A new release of Fox is available ! Check the new spacegroup explorer (see 
http://vincefn.net/Fox/Manual/ProfileFitting) and all the other new 
features !

  Download the new version from:
http://sourceforge.net/project/platformdownload.php?group_id=27546

  Note: if you have not-too-ancient version of Fox, then the menu 
"Help->Check for Updates" should tell you a new version is available too !

   Please report any issue with this new version.

  Here is the Changelog:
#### 1.8.0 - January 2009 (Revision #1080)
NEW FEATURES
   * Add a "spacegroup explorer" feature to the profile fitting
     widget, trying all spacegroups compatible with the unit cell,
     and calculating the corresponding Rwp and GoP.
   * Manual selection of profile parameters is now possible during
     profile fitting.
   * Add powder pattern -> Fullprof export (creates .pcr and .dat)
   * Add the ability to convert a list of atoms to a Molecule.
   * Mac version is now provided as a universal binary

IMPROVEMENTS
   * More optimized integration intervals for powder pattern
   * Allow choosing the number of peaks used for manual indexing
   * Avoid identical triclinic unit cells
   * Fox can now more easily be compiled with shared libraries for
     wxWidgets, fftw, (free)glut and newmat
   * Enable compilation with the unicode version of wxWidgets

BUG FIXES
   * Correctly handle change of Crystal for powder patterns,
     regenerate HKL list.
   * Correctly handle change of spacegroups during profile fitting

	Vincent
-- 
Vincent Favre-Nicolin

CEA Grenoble/INAC/SP2M			http://inac.cea.fr
Univ. Joseph Fourier (Grenoble) http://www.ujf-grenoble.fr

ObjCryst & Fox			http://objcryst.sf.net/Fox

[Objcryst-foxx] Fox website back online

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

	Hi,

   As you may have noticed the Fox wiki was unavailable after a server 
migration at sourceforge. I could not restore the wiki on their new servers, 
so the wiki is now available from my domain:

http://vincefn.net/Fox/

  If you go to the old site, you should be automatically redirected to the 
corresponding page on the new one.

  This site should be faster (at least from Europe), but let me know of any 
issue with it.

	Vincent
-- 
Vincent Favre-Nicolin

CEA Grenoble/INAC/SP2M			http://inac.cea.fr
Univ. Joseph Fourier (Grenoble) http://www.ujf-grenoble.fr

ObjCryst & Fox			http://vincefn.net/Fox

[Objcryst-foxx] Fox test version, with Fullprof export

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

	Hi,

   A new test version of Fox is available, with two new features:

* Fullprof export: an 'export' menu has been added to powder pattern objects, 
and can be used to create a .pcr and a .dat file. See the wiki documentation:
http://objcryst.sourceforge.net/Fox/Manual/Powder#export

Sorry, no export to gsas yet

* the ability to transform a list of individual atoms to a Molecule, using the 
Crystal menu "Scatterer->Convert atoms to a Molecule". This is mostly useful 
when opening a CIF file for a molecular compound.

  and a few other changes, see:
http://objcryst.sourceforge.net/Fox/Changelog

	Please report any problem or suggestion with these features
-- 
Vincent Favre-Nicolin
CEA Grenoble/INAC/SP2M			http://inac.cea.fr
Univ. Joseph Fourier (Grenoble) http://www.ujf-grenoble.fr
ObjCryst & Fox			http://objcryst.sf.net/Fox

[Objcryst-foxx] New FOX release 1.7.7

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

	Hi,

  There is a new Fox version available, recommended for all users :

   Among other changes it fixes two bugs:
(1) sometimes Fox would freeze after a long optimisation under windows
(2) some xml files could not be read back by Fox (the new version should be 
able to read all xml files, even those with NaN values in them.)

  Download the new version from:
http://sourceforge.net/project/platformdownload.php?group_id=27546

   (MacOS X ppc version is not yet available - only intel)

Changelog:
#### 1.7.7 - June 2008 (Revision #1013)
NEW FEATURES
   * Import single crystal data from CIF
   * Use M(n) for indexing scores, with n=20 as default

IMPROVEMENTS
   * Faster Le Bail
   * Improved triclinic indexing

BUG FIXES
   * Correct Fourier maps listing, when the 3D crystal view is
     opened during the Le Bail extraction
   * Fix freezing of optimization during long runs on windows.
   * Handle case when scale factors or intensities would be written
     as NaN in xml files.
   * Correctly add/remove Fourier maps


	Vincent
-- 
Vincent Favre-Nicolin

[Objcryst-foxx] New Fox release - 1.7.6.2 (#996)

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

	Hi,

  I just uploaded a new version of Fox. it adds a few features (Fourier maps 
for single crystal data, persistent resolution for Fourier maps using 
extracted intensities), and fixes a few bugs (notably with auto-indexing and 
related to locks/crashes under Linux with 3D display during the 
optimisation).

  Update is strongly recommended !

NOTE: I am currently testing using molecular dynamics to solve the 
conformation of flexible molecules with internal constraintes (e.g. flexible 
cycles with > 6 atoms). I have a few test data, but if you have more it could 
be useful. I hope to have a beta version soon.

  You can get the new version from :
http://sourceforge.net/project/platformdownload.php?group_id=27546

Recent changes:
#### 1.7.6.2 - April 2008 (Revision #996)
NEW FEATURES
   * Support Fourier maps for single crystal data
   * Display Fourier maps with the original resolution used for the
     extraction, no matter what resolution is used afterwards
     (e.g. during the optimisation)

IMPROVEMENTS
   * More efficient random moves for molecules, particularly for
     large molecules or with flexible cycles.
   * Better automatic changes of temperature for parallel tempering
   * Linux: enable compilation using "make -jN" (j2, j4...)
   * Nicer atom drawing. Force double buffering

BUG FIXES
   * Fixed incorrect formula for sample displacement
   * Linux: avoid lock of optimisation when 3D view is opened
   * Correct monoclinic indexing
   * Fix issue with manual auto-indexing
   * Disable auto-check for updates (could crash under Linux when no
     network can be reached)

   The full list of changes can be read on:
http://objcryst.sourceforge.net/Fox/Changelog

-- 
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] new Fox version - 1.7.5.3, bugfix

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

	Hi,

  A few days ago I made a new release for Fox, which fixes a few bugs. 

  The most important bug corrected was that the powder pattern was not 
computed when the first peak was before the beginning of the pattern (thanks 
to Bente Lebech for reporting this, and to Jan van Mechelen for other 
reports).

  You can get the new version from :
http://sourceforge.net/project/platformdownload.php?group_id=27546

  As always, suggestions about Fox development are welcome !

	Vincent
-- 
Vincent Favre-Nicolin
Université Joseph Fourier
http://vincefn.net
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] New Fox release

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

	Dear all,

   After a few fixes here is the new version of Fox, which you can get from:

http://sourceforge.net/project/platformdownload.php?group_id=27546

   The list of changes can be read on:
http://objcryst.sourceforge.net/Fox/Changelog


   Please report any issue with this new version, especially if you use Fox on 
a multi-core processor (Fox does not take advantage of multiple cores for the 
optimization but the parallel execution of some parts of the code could 
trigger new bugs - so far my tests on dual cores show no problem).

	Cheers,
		Vincent
-- 
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

Re: [Objcryst-foxx] New Fox release

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

	Hi,

  I've found a small but annoying bug under Linux, which may affect other 
platforms as well so I've pulled the new version. I won't be able to fix this 
until a few days, unfortunately.

   Sorry about the inconvenience... You can still watch the Fourier film in 
the meantime - 
http://vincefn.net/Fox-FourierMapEvolution-mpeg4.avi            (10Mo)

	Vincent
-- 
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] New Fox release

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

	Dear all,

   A new version of Fox is out. This is a mandatory update due to a bug 
observed in some spacegroup settings (thanks to Jan van Mechelen for careful 
testing).

  Get the new version from:
http://sourceforge.net/project/platformdownload.php?group_id=27546

   People already using the last beta version should see a more stable profile 
fitting, auto-indexing support for triclinic cells (slow), and the extracted 
structure factors are now saved in the xml files - see the full changelog 
below.

   If you want to see how useful a difference Fourier map can be during an 
optimization, you can watch the following movie - it lasts for 1 minute and 
shows the evolution of + and - difference Fourier maps as the algorithm 
converges towards the correct structure of Cimetidine :
http://vincefn.net/Fox-FourierMapEvolution-mpeg4.avi		(10Mo)


   Please report any issue with this new release. Notably, MacOS versions are 
yet untested.

   Full changelog: 
#### 1.7.5 - February 2007 (Revision #956)
NEW FEATURES
   * Add support to compute Fourier maps (observed, difference),
     with a "live" update during optimization
   * Profile fitting and Le Bail extraction is now directly 
     available from a right-click on the powder pattern graph.
   * Support for Intel macs
   * Indexing triclinic lattices
   * Explore centered lattices during auto-indexing
   * LeBail-extracted structure factors are now saved in the xml file

IMPROVEMENTS
   * More stable profile fitting
   * Linux: keyboard shortcuts are working again

BUG FIXES
   * Fixed incorrect computation of dynamical occupancy correction
     in some asymmetric unit configurations
   * Fixed crash when switching labels on/off during optimization
   * Fixed windows crash when removing atoms in a Molecule/Polyhedron

-- 
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] New Fox for MacOS X

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

	Dear all,

  For those who use Fox on Mac OSX, there is a new version available - it=20
corrects a bug which led to a crash at the end of the optimization dependin=
g=20
on the computer's configuration.

  Get it (ppc/i386) from:
http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D=
162603&release_id=3D353835

   And many thanks to Vladimir Jorik for testing many versions to correct t=
his=20
bug !

	Vincent
=2D-=20
Vincent Favre-Nicolin
Universit=C3=A9 Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

Re: [Objcryst-foxx] New FOX Beta version - LINUX update

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

  This concerns just linux users:=20

  I had forgotten the small part which compiles the fftw library - to=20
correctly compile Fox you can either:

* do 'svn update' from the top Fox directory and re-start the compilation
* download the new package (revision 931):
https://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=
=3D162603&release_id=3D353844

	Vincent
=2D-=20
Vincent Favre-Nicolin
Universit=C3=A9 Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] New FOX Beta version - with Fourier maps

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

	A happy New Year to all of you !

  And to start 2008 nicely, here's a new version of Fox to test. Get it fro=
m:
http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D=
162603

There are a few new features:

* Fourier maps : Fox can now compute obs, calc and difference maps from=20
available data, and you can see them updated as the optimization goes on.=20
See :
http://objcryst.sourceforge.net/Fox/Manual/Crystal#Fourier

*  the other important feature is hidden - Fox will now silently check for=
=20
updates, and will warn the user if a new version fixing an important bug is=
=20
available. This should be transparent to the user, but you can also directl=
y=20
check using the Help menu to get more detailed information (Fox will only=20
warn you automatically if a major bug is found, which won't happen too=20
often). Note that this does not work yet under windows - an issue with=20
wxWidgets.

* the profile fitting and Le Bail extraction dialog is now directly availab=
le=20
from a right-click on the powder pattern graph.

* A version for Intel Macs is also available

  Let me know of any issues with this beta version.

	Cheers,
		Vincent
=2D-=20
Vincent Favre-Nicolin
Universit=C3=A9 Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net

[Objcryst-foxx] New Fox release -1.7.1.1 - mandatory update !

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

	Dear all,

   I have put a new release (1.7.1.1) of Fox, you can download it from:

http://sourceforge.net/project/platformdownload.php?group_id=3D27546

   This is the first 'official' version supporting auto-indexing and profil=
e=20
fitting ! It is also more responsive during an optimisation. See the=20
Changelog:
http://objcryst.sourceforge.net/Fox/Changelog


  BUGFIX : All users *must* update - last week a bug was reported involving=
=20
distance calculations and dynamical occupancy correction for high symmetry,=
=20
centered spacegroups. It would not prevent finding a solution but would mak=
e=20
it more difficult - fixed atoms in some special positions would have a wron=
g=20
dynamical occupancy.

  Linux users should download the new .tar.bz2, as updating through svn wou=
ld=20
not download the new wxGTK (2.8.7) version, which is required to fix a few=
=20
bugs between wxWidgets and GTK+

   Sorry, no MacOS X version yet - the compiled Universal binary is buggy a=
nd=20
I have no way to test it immediately - email me privately if you still need=
 a=20
binary.

	Cheers,
		Vincent
=2D-=20
Vincent Favre-Nicolin
Universit=C3=A9 Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net