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From: Vincent Favre-N. <vi...@us...> - 2007-06-09 22:03:12
|
Dear all, =20 I have now added profile fitting and Le Bail extraction to Fox. This can= be=20 used to get better profiles before starting the global optimisation, and al= so=20 to check on the validity of indexing solutions (by looking at the Rwp and G= oF=20 values obtained from different cells). Download the new TEST version of Fox from:=20 http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D= 162603 and read the corresponding manual page @: http://objcryst.sourceforge.net/Fox/Manual/ProfileFitting and the updated indexing page @: http://objcryst.sourceforge.net/Fox/Manual/Indexing (now automatic Le Bail+profile fittingcan be done when selecting each=20 solution). Note that only pseudo-voigt is yet supported, not the DE-PV profile for T= OF. Let me know of any problem or suggestion you may have ! Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2007-04-29 23:04:26
|
Dear all, It's not finished yet (triclinic being mostly not functional) but you ca= n=20 test indexing using Fox. Download the new TEST version of Fox from:=20 http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D= 162603 and read the corresponding manual page @: http://objcryst.sourceforge.net/Fox/Manual/Indexing Please let me know how useful this is, bugs you can find, desired featur= es,=20 etc... The main aim after this is to make triclinic working better, and=20 couple this to profile-fitting (Le Bail / Pawley). If you have a non-triclinic pattern which cannot be indexed, don't hesit= ate=20 to send it to me so that I can test against it. Later I'll put a page with all the test patterns I've used (mostly the=20 patterns available from the IUCr journals these last few years - all seem t= o=20 index nicely and quickly) and comments for each test. =20 Cheers, Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2007-03-11 22:24:57
|
Dear all, It has been a (too) long time since the last official version of Fox ! S= o=20 here is version 1.7.0 (svn revision 855).=20 A few features and bugfixes have been added since the last beta versions= ,=20 so everybody should upgrade ! You can see the Changelog at: http://objcryst.sourceforge.net/Fox/Changelog You can download the new version from: http://sourceforge.net/project/platformdownload.php?group_id=3D27546 Note that along the Fox packages there the Fox manual in pdf as a separa= te=20 download - it is nothing more than a pdf transcript of the Fox wiki, but it= =20 can be handy to print out. I'll wait a few days to see if any bug is reported, before announcing it= on=20 the powder diffraction mailing-lists. After that, I'll go back to work on new features: =2D Auto-indexing: it is mostly working, but still to be tested for all=20 lattices, so it is deactivated in the 1.7.0 release =2D Mixed occupancy sites =2D Unicode version I'll put up beta (test) versions for you to test all this. =09 Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2007-01-16 20:45:27
|
Happy new year ! This year should bring interesting features for Fox: indexing is finshed= ,=20 profile fitting will follow, support for unicode, atoms with mixed=20 occupancy,... I corrected a few bugs in the last few weeks, for distance calculations,= =20 TOF... Unfortunately the Fox version released at the end of December (19th)= =20 includes a major bug which prevents any optimisation (even pbso4 cannot be= =20 solved !). Bottom line: All users must upgrade to the current version (20070109 for= =20 Linux & windows, 20010111 for OSX. If I don't get any bug report I'll make= =20 this the "stable" release. Auto-indexing can be tried on the OSX and Linux version, but is deactiva= ted=20 in the windows version - I still need to add profile fitting to make it=20 self-sufficient - after indexing and peak position refinement the cell=20 parameters are not yet precise enough to launch the optimisation. Cheers, Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2006-11-14 22:04:50
|
Hola, A new version of Fox (again). All people who use spacegroup which genera= te=20 a parallelepipedic asymmetric unit cell which includes negative coordinates= =20 *and* use dynamical occupancy correction must update, as the distance=20 calculations were wrong. This concerns 16 spacegroups: 91,98,141,148,164,167,178,183,186,191,194,198,205,214,220,230 This version also improves CIF import, as some files (e.g. from fullprof= )=20 were not correctly imported. I'll try to update new MacOSX files in a few days as well. =20 Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2006-11-12 21:36:38
|
Dear all, A new beta version of Fox is out - this one enables importing CIF files= =20 into Fox, which was a "most wanted" feature. Of course I expect a few=20 glitches with it - I have only tested a few crystal structures and powder=20 patterns with it. The nice thing is that you can open the CIF file on the launch of Fox, s= o=20 you should be able to right-click on a cif file to choose "open with...Fox"= =20 or drag & drop on the Fox application icon (may not work on MacOSX). If you have enabled automatic opening of the 3D structure and powder=20 pattern graph using the Fox preferences=20 (http://objcryst.sourceforge.net/Fox/Manual/Preferences), then you can see= =20 the structure (or powder pattern) immediately ! See http://objcryst.sourceforge.net/Fox/Manual/CIF for more info about wh= ich=20 CIF tags are actually parsed. New Fox available from: http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D= 162603 And please report any CIF that is not correctly opened and should be ! Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2006-10-29 21:31:00
|
Dear all, (I'm off to the APS in Chicago tomorrow morning for a week of coherent=20 diffraction so I hope the new release is fine - I'll try to read my email=20 anyway). There's a new release of Fox available from : http://sourceforge.net/project/showfiles.php?group_id=3D27546 (in the "Test versions" - but it should be relatively stable). It fixes two major bugs: =2D Rhomboedral/Hexagonal unit cells were not always correctly handled ; th= is=20 works now and you can read how to choose your favorite settings on the wiki: http://objcryst.sourceforge.net/Fox/FoxRefGUICrystal#head-fa3bd97db76a86c12= 2330c5a5df9bc69b6bdbc5b =2D single crystal data did not properly save the scale factor, so that mul= tiple=20 optimizations and reloading from xml file did not work as expected (the R=20 factors would look very wrong when reloading one 'solution'). And a few new features: =2D Preferences: you can now choose if you want to automatically open the 3= D=20 crysta view, the powder pattern to display the atom names, the reflection=20 indices, the full or assymetric unit cell, etc... Note that you must open t= he=20 corresponding window at least once to access the preferences (i.e. no=20 preferences can be chose for the 3D crystal view until you have opened at=20 least once this view with the new version). =2D Compressed data file: you can used compressed files - these are just xm= l=20 files compressed with gzip so you can uncompress them if you want to modify= =20 them. Use the preferences to trigger the default use of the compression. A few other new features (intensities for groups of reflections on singl= e=20 crystal data, electron diffraction) are experimental, so I'll really announ= ce=20 them later on. Hope that can make Fox more enjoyable. Cheers, Vincent =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2006-02-28 21:08:48
|
Hola, I have posted new versions of Fox (Linux, Mac, windows) on Sourceforge.= =20 Compared to the last version in November, this one fixes a few bugs: - crash when re-opening a crystal structures 3D view (linux) - memory growth when running for a *long* time with a ZScatterer object + a number of other small bugs. And a new feature: =2D ability to export a Molecule object to a "named" z-matrix", i.e. a z-ma= trix=20 where names of atoms are used rather than their indices. This allows an=20 easier direct manipulation of the z-matrix. Of course the associated import= =20 is also available Note that the wiki documentation has been updated for the new version. T= his=20 means that this should be the final 1.7 version unless something comes up ! Get the new Fox from: http://objcryst.sourceforge.net/Fox/ Also, for developers, the source code of ObjCryst++/ Fox is now stored= =20 using subversion (svn) rather than cvs, still on sourceforge. See=20 http://objcryst.sourceforge.net/Fox/FoxSVN. The cvs still exists but will n= ot=20 be updated. Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2005-11-06 14:33:16
|
Hi all, Another beta version available from http://objcryst.sourceforge.net/Fox/FoxDevelopment Changes: =2D The automatic Bayesian background is now *much* faster, and you can edi= t the=20 background points from the graphical interface (both position and intensity= ).=20 You can also re-generate an automatic background, which is useful if you wa= nt=20 to change the number of points =2D Editing dihedral angle restraints and rigid groups should now work corr= ectly =2D Fox in command-line mode can now load files without the "-i" option, i.= e.=20 the following command will work to load the "test.xml" file Fox test.xml The latter should make *much* more natural to use Fox from a directory=20 browser (i.e. right-clicking on a file and telling the OS to open it with F= ox=20 should work). Oh, and the wiki is now directly accessible from=20 http://objcryst.sourceforge.net/Fox/ =2E.. which means that the old html pages have been removed. Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2005-11-01 09:52:57
|
Hola, The new Fox beta is also available for OSX. I have compiled two versions= =2E=20 The first is compiled for G3 and should run on any powermac, theoretically= =20 with any version > 10.2 - but I would very much like to know if it actually= =20 runs on 10.2.8 and 10.3.9 (the latest 10.2 and 10.3 versions). I only have= =20 10.4.2 computer to test on. The second (with "-G4-G5") is a multiple-achitecture binary, which shoul= d=20 have optimizations for *both* G4 and G5 (yes, with altivec and=20 auto-vectorization on, but so far auto-vectorization should not have too mu= ch=20 effect). However, I have already seen it seems to crash on an iMac G4 800... I would be extremely glad if you could tell me whether it runs on your=20 computer (you have to launch an optimization to test), and at which speed.= =20 =46or this please run in "speedtest" mode, once the images are mounted, fro= m a=20 Console.app: /Volumes/Fox-20051031CVS/Fox.app/Contents/MacOS/Fox --speedtest and (for the G4-G5 version) /Volumes/Fox-20051031CVS-G4-G5/Fox.app/Contents/MacOS/Fox --speedtest I am only interested in the last 20 lines giving the summary of the=20 performance, to see if it's useful to do the multiple compilation. Please include in your report the exact system and processor you are usi= ng=20 (e.g. OSX 10.3.9 with G4 1.0GHz). I would really like to have both versions= =20 tested on a G5 - I can't do that remotely. Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2005-11-01 09:24:44
|
Bonjour =E0 tous, A new beta version for Fox is up: * The most important change is that the initialization of the Molecule stre= tch=20 Mode is *much* faster for large Molecule - i.e. when launching an=20 optimization you do not have to wait for ages if you have a lot (>100) of=20 Atoms. * Also, it is possible to use the "multiple runs" feature in console mode. * The Rigid groups can be edited directly * When re-launching a "multiple run", the previous solutions will not be=20 erased (unless any of the refined object has been changed manually) For more information (features, download), see http://objcryst.sourceforge.net/cgi-bin/moin.cgi/FoxDevelopment =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2005-10-18 20:34:40
|
Hola, a new beta is up. No major change - you should only update if you are=20 inputting atoms in a Molecule object *manually* and therefore need to=20 optimize the starting configuration. This did not work in previous betas. http://objcryst.sourceforge.net/cgi-bin/moin.cgi/FoxDevelopment Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2005-10-17 22:06:50
|
Dear all, There is a new beta version of Fox. Changes include: * Better restraints for Molecule objects: now when there are conflicting=20 restraints (e.g. several bond angles trying to affect 1 atom position), the= =20 Molecule will correctly manage to minimize the restraint. Same when flippin= g=20 atom groups. This should be *really* much better to keep user restraints... * Scattering Powers parameters are now all displayed in a single window=20 (except for the symbol). this includes antibump and bond valence parameters= ,=20 which are finally directly accessible Also in the windows precompiled version, I have disabled the console=20 output, which seems to speed up Fox. =46or more details and link to download, see: http://objcryst.sourceforge.net/cgi-bin/moin.cgi/FoxDevelopment Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2005-10-03 08:45:15
|
Hi, It seems that downloading files from sourceforge has a few problems. Whe= n=20 you reach the sourceforge page: http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D= 162603 After clicking on the "Download Fox-20051002CVS.zip", you should be able to= =20 select the download server from a long list... Right now there is only one= =20 server available from Russia, and it does not work... In the meantime you can download directly from the Paris and Zurich=20 servers: http://ovh.dl.sourceforge.net/sourceforge/objcryst/Fox-20051002CVS.zip http://switch.dl.sourceforge.net/sourceforge/objcryst/Fox-20051002CVS.zip VIncent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2005-10-02 22:29:38
|
Hi all, There is a new beta version of Fox available for windows. Most important= =20 changes from the previous beta are: ######## * fix for an important bug, by which wrong multiplicities were computed for= =20 acentric reflections). This affected all beta versions since july 7th, 2005= =2E=20 All people using these *must* upgrade. Optimizations for all=20 non-centrosymmetric reflections will be wrong. * New Molecule modelling and graphical interface, for a better user-control= of=20 the molecule geometry, and easier use of larger molecules. Detailed information about the new features can be found on the Fox=20 development page of the Fox wiki: http://objcryst.sourceforge.net/cgi-bin/moin.cgi/FoxDevelopment ######## =46or windows, you can get the betw version from: http://sourceforge.net/project/showfiles.php?group_id=3D27546&package_id=3D= 162603 =46or Linux, just go to the Fox directory, do a 'make update' and recompile. Sorry, no MacOS X updated version yet... Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2005-07-22 14:48:20
|
Hello again, ####### Fox on Mac OS X ########### After a long struggle which began a year ago, Fox is now working on MacOS= X.=20 The first version (with the help of Ch. Baerlocher) allowed Fox to work, bu= t=20 only using an GTK/X11 widget set, i.e. not with the native "aqua" look. of= =20 MacOS. I have laid my hands on XCode 2.1 yesterday and managed to compile i= t=20 natively. It seems to run reasonably well, with the small glitches: =2D The 3D structure is not shown when the 3D window ios initially opened (= you=20 need to move it with the mouse to show it) =2D When optimizing, it can take some time (a few seconds - sometimes up to= 30s)=20 before clicking on a window or button will work - but so far it always work. Let me know if you can try it. You can download the compressed disk imag= e=20 with the application (compiled on a G4, so only for G4 or G5) from: http://objcryst.sourceforge.net/test/Fox-CVS20050721.dmg ######### Linux RPM ############# Some people have asked for a rpm-based installation under Linux. It's=20 practically ready, except that I have to sort out the dependencies for each= =20 distribution. There is a rpm for Mandriva 2005, as well as the correspondin= g=20 source rpm, and a source rpm for Fedora Core 4 @ http://objcryst.sourceforge.net/test/ Please let me know if you are interested to test these. It may require ro= ot=20 access on your linux machine to recompile the rpm from the src.rpm. Cheers, Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2005-07-22 14:37:35
|
Hi all, It has been a long time since the last news about Fox. A new version is=20 coming, with numerous changes (support for neutron TOF, multiple solutions,= =20 support for MacOS X, better Molecule support, ...). I will announce the nex= t=20 test version of Fox soon. In the meantime, here are some news: ############### FOX WIKI ################ * The FOX documentation is now stored in a wiki. Which means that it is edi= ted=20 online and *anyone* can contribute to it. Right now it mostly contains the= =20 same information as the old manual, plus more compilation information. You= =20 can see it at: http://objcryst.sourceforge.net/cgi-bin/moin.cgi The newest page is the list of all publications with structures solved usin= g=20 =46ox: http://objcryst.sourceforge.net/cgi-bin/moin.cgi/FoxBiblioStructures Please feel free to edit the page to add your structure, or correct the= =20 references if I made a mistake. ############### FOX In Florence ################ There will be two presentations about Fox at the IUCr'2005 conference in= =20 =46irenze: * Thursday 25th august, @ 14h25, In the MS25 " Structure Determination fro= m=20 Powder Diffraction Data (Organics) ", I will be talking about the latest ne= ws=20 about Fox, with more emphasis about organics * Sunday 28th August - 10:00 to 12:00, in the "Software Fayre", Radovan Cer= ny=20 and myself will be presenting and demonstrating structure solving using Fox= =2E=20 This will be probably the best place to demand new features, discuss the=20 future of Fox as well ! Best, =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2004-07-19 22:24:39
|
Hi (again) I am also trying to find all structures solved by Fox, for which publi=20 references are available. Here are thos I found. I'd be glad if you have=20 others. Please correct me if I made a few errors in the list. Materials Letters 58 (2004) 672 678 Ab initio structural determination of 2-(2-pyridyl)imino-N-(2-thiazolin-2-yl)thiazolidine from powder diffraction data L.M. Gonza=B4lez-Me=B4ndeza, F.L. Cumbrerab,*, M.C. Garc1=B4a-Cuestab, =46. Sa=B4nchez-Bajoc, A.L. Ortizc, F.J. Higes-Rolandod, F. Luna-Giles (Badajoz, Spain) New solid state Ni(II)-famotidine square-planar complex: powder diffraction and spectroscopic studies Malgorzata Baranska a,*, Wiesaw Lasocha a, Henryk KozBowski b, Leonard M. Proniewicz a,c,* (Krakow, Poland & Wroclaw, Poland) Journal of Inorganic Biochemistry, Volume 98, Issue 6, June 2004, Pages=20 995-1001=20 Zeitschrift f=FCr anorganische und allgemeine Chemie Volume 630, Issue 4, 2= 004.=20 Pages 597-603 http://www3.interscience.wiley.com/cgi-bin/fulltext/107637041/PDFSTART Synthesis and Characterization of some Unsymmetrical Schiff Base Ligands an= d=20 their Nickel(II) Complexes Incorporating o-Phenylenediimine Units Ewa M. Opozda, Dr. *, Wiesaw Lasocha, Barbara Wodarczyk-Gajdab (Krak=F3w,Po= land) J. Phys.: Condens. Matter 16 (2004) 3005-3013 LiSrAlF6 with the LiBaCrF6-type structure Andrzej Grzechnik1,5, Vladimir Dmitriev2, Hans-PeterWeber2,3,Jean-Yves=20 Gesland4 and Sander van Smaalen1=20 (Bayreuth, Germany & ESRF & Lausanne, Swizerland & Le Mans, France) J. Phys.: Condens. Matter 16 (2004) 1033-1043 The crystal structures of pressure-induced LiSrAlF6-II and LiCaAlF6-II Andrzej Grzechnik1,5, Vladimir Dmitriev2, Hans-PeterWeber2,3,Jean-Yves=20 Gesland4 and Sander van Smaalen1 (Bayreuth, Germany & ESRF & Lausanne, Swizerland & Le Mans, France) Acta Cryst. (2004). B60, 453-460 http://journals.iucr.org/b/issues/2004/04/00/lc5007/index.html Ab initio structure determination of the hygroscopic anhydrous form of=20 [alpha]-lactose by powder X-ray diffraction C. Platteau, J. Lefebvre, F. Affouard and P. Derollez (Lille, France) J. Appl. Cryst. (2004). 37, 464=B1471 Ab initio structure determination of m-toluidine [3-methylbenzenamine] by=20 powder X-ray diffraction Mwaffak Rukiah,a=B3 Jacques Lefebvre,a* Marc Descamps,a Stephanie Hemona an= d=20 Alexander Dzyabchenkob (Lille, France & Moscow, Russia) Acta Cryst. (2004). B60, 272-281 Mg(1+x)Ir(1-x) (x =3D 0, 0.037 and 0.054), a binary intermetallic compound = with=20 a new orthorhombic structure type determined from powder and single-crystal= =20 X-ray diffraction R. Cern=FD, G. Renaudin, V. Favre-Nicolin, V. Hlukhyy and R. P=F6ttgen (Gen= eva,=20 Switzerland & M=FCnster, Germany) Acta Cryst. (2003). B59, 753-759 Structures of potassium, sodium and lithium bis(oxalato)borate salts from=20 powder diffraction data [ only Li[B(C2O4)2]H2O solved with Fox] Peter Y. Zavalij,* Shoufeng Yang and M. Stanley Whittingham (New York, USA) Hydrogenation of oxygen-stabilized Zr3NiOx compounds Journal of Alloys and Compounds, Volume 360, Issues 1-2, 6 October 2003, Pa= ges=20 173-182=20 Yu. Zavaliy , R. Cerny , I.V. Kovalchuck , I.V. Saldan (Lviv, Ukraine & Gen= eva=20 Switzerland) Journal of Alloys and Compounds 354 (2003) 143-147 The structure of Li3AlD6 H.W. Brinks , B.C. Hauback (Kjeller , Norway) LaMg2NiH7 , a novel quaternary metal hydride containing tetrahedral 42 [NiH4]4- complexes and hydride anions Journal of Alloys and Compounds, Volume 350, Issues 1-2, 17 February 2003,= =20 Pages 145-150 G. Renaudin, L. Guenee , K. Yvon (Geneva, Switzerland) Synthesis, crystal structure and hydrogenation properties of the ternary=20 compounds LaNi4Mg and NdNi4Mg Journal of Alloys and Compounds, Volume 348, Issues 1-2, 13 January 2003,=20 Pages 129-137 L. Gu=E9n=E9e, V. Favre-Nicolin and K. Yvon (Geneva, Switzerland) Synthesis, crystal structure and hydrogenation properties of the novel meta= l=20 compound LaNi2Mn3 Journal of Alloys and Compounds, Volume 348, Issues 1-2, 13 January 2003,=20 Pages 176-183 L. Gu=E9n=E9e and K. Yvon (Geneva, Switzerland) CHEM. COMMUN., 2002, 808-809 Al2(CH3PO3)3 Structure solution of a novel aluminium methylphosphonate using a new simulated annealing program and powder X-ray diffraction data=20 Mark Edgar,a Vinton J. Carter,a David P. Tunstall,b Paramjit Grewal,c Vince= nt=20 =46avre-Nicolin,d Paul A. Cox,c Philip Lightfoota and Paul A. Wright (St Andrews, UK & ESRF, Franc= e) Synthesis and structure of an orthorhombic low-pressure polymorph of caesiu= m=20 magnesium hydride, CsMgH3 Journal of Alloys and Compounds, Volume 353, Issues 1-2, 7 April 2003, Page= s=20 175-179 G. Renaudin, B. Bertheville and K. Yvon (Geneva, Switzerland) Lithium boro-hydride LiBH4: I. Crystal structure Journal of Alloys and Compounds, Volume 346, Issues 1-2, 18 November 2002,= =20 Pages 200-205 J-Ph. Souli=E9, G. Renaudin, R. Cern=FD and K. Yvon (Geneva, Switzerland) Acta Cryst. (2002). C58, i31-i32=20 A tetragonal polymorph of caesium hydroxide monohydrate, CsOH=B7H2O, from X= =2Dray=20 powder data R. Cern=FD, V. Favre-Nicolin and B. Bertheville (Geneva, Switzerland) #############Conferences############# http://www.xray.cz/epdic/abstracts/211.htm http://www.xray.cz/epdic/abstracts/220.htm http://www.xray.cz/epdic/abstracts/325.htm http://www.xray.cz/epdic/abstracts/412.htm =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Vincent Favre-N. <vi...@us...> - 2004-07-19 22:21:23
|
Hi all, There is a *test* version for Fox available. This gives very significant= =20 speed improvements in speed, both from a number of code changes,=20 and also from the use of dear microsoft's visual c++ 2003 compiler=20 (which is now available freely). windows users can get the test version fro= m: ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test/ Speed increase should be 2x to more than 3x ! Also, this adds new experimental code which adapts the rotation=20 amplitude of free rotations depending on the number of atoms=20 moved, so this should really improve things for mdeium to large molecules. There will not be a new official release till some time (I'd like to add a few things like the requested support for TOF data) so I encourage=20 everybody to upgrade and report any new problem ! Other interesting=20 reports include: =2D final result of "Fox --speedtest" from the command line (along with=20 your computer processor specs) =2D whether people experimenting trouble with 3D display when 3D=20 acceleration is ON still have problems (I don't expect any change, but who knows...) Linux users can upgrade using the CVS. Due to cvs changes,=20 you'll need to type the following in the Fox directory first (please do *no= t*=20 run this as root, just in case): perl -pi -e 's|cvs.objcryst.sourceforge.net|cvs.sourceforge.net|g' `find . = =2Dname Root` Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2003-12-14 13:46:41
|
Hi, There is a new version of FOX (for ab initio structure determination fro= m=20 powder diffraction) available. This version highlights are: =2D gives the user (you!) more control on the flexibility on the "Molecule"= =20 scatterer which has replaced the z-matrix approach =2D fixes a major bug which caused all peaks to be randomly displaced in th= e=20 pattern calculation, by up to 2 pixels. This is essentially noticeable for= =20 low-resolution patterns (tests of peak positions accuracy had of course bee= n=20 done at high resolution...). However, the use of 'integrated' peaks=20 evaluation made the structure solution not too sensitive to this error. In= =20 practice, you should see a significant improvement on the computed Rwp and = R=20 factors (computed on the full profile), but little on the Chi^2 (uses the=20 integrated intensities). Thanks to Michal Hu=C5=A1=C3=A1k for his thorough = testing &=20 reporting. =2D better 3D view and POV-Ray export (see=20 http://objcryst.sourceforge.net/Fox/screenshot.html) Also note that there will be small Fox article in the upcoming IUCr=20 Commission on Powder Diffraction (CPD) NewsLetter, with a few nice examples= =20 of structures solved using Fox... Fox home page: http://objcryst.sourceforge.net/ Direct download (windows users get the Fox-20031213.zip file, other file= s=20 are source code for windows and Linux): http://sourceforge.net/project/showfiles.php?group_id=3D27546&release_id=3D= 203604 or download from the CCP14 ftp mirrors: 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/ Full Changelog: #### 1.6.0.2 - december 2003 NEW FEATURES * Added the export to a POV-Ray file to create a Ray-traced view of the 3D Crystal window, with support for both Crystal structure and Fourier maps. * Added more user control on the fexibility of a Molecule: - Added "Rigid Body" and "User-Chosen Free Torsion" choices for the flexibility model of the Molecule. - Also added an option to disable the optimisation of the orientation of the Molecule (only useful for "Rigid Body" mode) - Give access to the delta and sigma parameters to calculate restraints, although users are HIGHLY advised not to change the default values unless they really know what they are doing Also, a Molecule will by default be less flexible than before * Added import of DSN6 Fourier maps, which can be created by forplot in GSAS. * Reverted to using GLUT under Linux to display atom labels in the OpenGL window, as some graphical drivers did not fare well with the new method. * Ability to remove several atoms/bonds/angles at the same time. When removing a bond, offer to remove the bond angles and dihedral angles using that bond. * Added reflection labels on the powder pattern graphical display. * Speed improvements by avoiding (more) recomputations. * Fox now uses wxWindows 2.4.x (no support for versions <2.4). * Added support for Cobalt X-Ray tube. Also, correctly save X-Ray tube parameters when they have been entered manually. * Fourier maps with negative contour values will now be highlighted towards negative values, for Fobs-Fcalc maps display. =20 BUG FIXES * The position of peaks on a powder pattern was randomly displaced by up to +/-2 pixels for each reflection. This could be serious for patterns recorded with a low resolution relatively to the peak widths, although the use of "integrated" Chi^2 and R-factors reduced the gravity of this bug. (thanks Michal Husak for serious testing and reporting) * In the CIF output, some atoms were wrongly labeled as being=20 overlapping with another identical element. * In the graphical display of powder patterns, improve the precison of the display. * Correct center of view coordinates when the center of the displayed structure is not at (0.5,0.5,0.5) =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2003-12-08 19:35:10
|
Hi, Title says it all. Thanks to Philippe Deniard for reporting the bug. Also= ,=20 CVS version should link OK with RedHat 9.0. update using CVS, or get a precompiled windows version from: ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test/ and soon @ http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/ http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/ Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2003-12-07 10:22:17
|
Bonjour, So far still no problems reported with the beta version, but I finally (= the=20 format is really strange, although probably ideal for all those computers=20 with punch cards) managed to add the import of Fourier maps with the DSN6=20 format, which is supported by forplot in GSAS/EXPGUI. You now have the choi= ce=20 to import Fourier maps in the *.grd format (using forgrid supplied by Brian= =20 Toby), or the .DN6 format which is in forplot. You can look at several=20 =46ourier maps and several contours at the same time, and export to pov-ray= =2E=20 See the garnet example at the top of the screenshots page: http://objcryst.sourceforge.net/Fox/screenshot.html#pov Also, a few glitches & inconsistencies in 3D display have been removed. = The=20 final version should be 1.6.0.1 update using CVS, or get a precompiled windows version from: ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test/ and soon @ http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/ http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/ NOTE: the ftp.unige.ch Fox repository is not available now as the server= is=20 being reinstalled, so use only the CCP14 mirrors Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2003-12-03 11:29:56
|
Hi All, Nobody has reported problems with the Fox beta version, so it should be = OK=20 for the official release at the end of the week. Nevertheless I had a bit of fun last week and added the ability to expor= t=20 the 3D view to a POV-Ray file (right-click in the 3D view to get the popup= =20 menu), e.g. see http://objcryst.sourceforge.net/Fox/screenshot.html#pov=20 (bottom of page). get the (hopefully final) version with POV-Ray support from ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test/ and soon @ http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/ http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/ NOTE: the ftp.unige.ch fox repository is not available now as the server= is=20 being reinstalled, so use only the CCP14 mirrors Cheers, Vincent PS: if in POV-Ray, the image obtained is reversed (left/right), please let = me=20 know which version of POV-Ray and which OS you are working on. =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2003-11-25 22:56:56
|
Hi all, There is an upcoming version of Fox with one major bugfix , plus numerou= s=20 imrovements, especially for people wanting to have more control on the=20 flexibility of Molecules they are working with. The major bug was that peak positions were incorrect by up to +/- 2 pixel= =20 (due to a correction in the wrong direction when comparing the true positio= n=20 to the nearest pixel position). This appears clearly on _low_ resolution=20 patterns (and of course accuracy testing was done on high resolution=20 patterns...). This can lead to significant improvements to previously =20 incorrectly calculated R and Rw, although the use of "integrated" Chi^2 and= =20 R-factors helped minimize this effect. *Many* thanks to Michal Hu=C5=A1=C3= =A1k for his=20 thorough testing & reporting. You can test this new version by updating from the CVS (if you compile=20 =46ox). Linux users will have to make sure the glut libarry is installed, a= nd=20 will need to copy the Fox/ObjCryst/rules-gnu.mak to Fox/ObjCryst/rules.mak)= ,=20 Also, Fox now supports only wxWindows 2.4+ (tested with 2.4.2) on both Linu= x=20 and windows. For those wanting a precompiled windows .exe, it can be found @ ftp://ftp.unige.ch/pub/soft/crystal/fox/test/ ftp://ftp.ccp14.ac.uk/ccp14/ftp-mirror/objcryst/test/ and soon @ http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/objcryst/test/ http://ccp14.semo.edu/ccp/ccp14/ftp-mirror/objcryst/test/ Fox Changelog goes: #### 1.5.1 - december 2003 NEW FEATURES * Added more user control on the fexibility of a Molecule: - Added "Rigid Body" and "User-Chosen Free Torsion" choices for the flexibility model of the Molecule. - Also added an option to disable the optimisation of the orientation of the Molecule (only useful for "Rigid Body" mode) - Give access to the delta and sigma parameters to calculate restraints, although users are HIGHLY advised not to change the default values unless they really know what they are doing Also, a Molecule will by default be less flexible than before * Reverted to using GLUT under Linux to display atom labels in the OpenGL window, as some graphical drivers did not fare well with the new method. * Ability to remove several atoms/bonds/angles at the same time. When removing a bond, offer to remove the bond angles and dihedral angles using that bond. * Added reflection labels on the powder pattern graphical display. * Speed improvements by avoiding (more) recomputations. * Fox now uses wxWindows 2.4.x (no support for versions <2.4). * Added support for Cobalt X-Ray tube. Also, correctly save X-Ray tube parameters when they have been entered manually. =20 BUG FIXES * The position of peaks on a powder pattern was randomly displaced by up to +/-2 pixels for each reflection. This could be serious for patterns recorded with a low resolution relatively to the peak widths, although the use of "integrated" Chi^2 and R-factors reduced the gravity of this bug. (thanks Michal Husak for serious testing and reporting) * In the CIF output, some atoms were wrongly labeled as being=20 overlapping with another identical element. * In the graphical display of powder patterns, improve the precison of the display. =2D-=20 Vincent Favre-Nicolin Universit=C3=A9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |
From: Favre-Nicolin V. <vi...@us...> - 2003-08-17 18:48:31
|
Hi, There is a new version of Fox available, essentially to fix two bugs=20 crashing Fox for specific bond angle values in a Molecule (thanks Simon=20 Parsons for reporting this). Also, it adds a scale factor for the AntiBump function if its value is to= o=20 small compared to the Chi^2 of the diffraction data. Note, however, that I= =20 recommend trying to solve structures *without* use of the AntiBump. I will be presenting Fox at the ECM in Durban, sunday morning at the sin= gle=20 crystal & powder diffraction workshop, and tuesday morning in the "Structur= e=20 Determination from Powder Diffraction" microsymposium. Fox can be downloaded from: http://sourceforge.net/project/showfiles.php?group_id=3D27546&release_id=3D= 167682 ftp://ftp.unige.ch/pub/soft/crystal/fox/ 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/ Vincent =2D-=20 Vincent Favre-Nicolin Universit=E9 Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net |