- cctbxbb - phenix-online.org

Re: [cctbxbb] Fail to extend space-group with centring translations
by Ralf W. Grosse-Kunstleve 11 Dec '06

11 Dec '06

> Luc, This is a key item in Ralphs reply: > > "You cannot change the rotation denominator (fixed at 1) for the > matrices processed by sgtbx.space_group. Therefore you cannot work > with, e.g. the pseudo-orthorhombic C-centered setting of a hexagonal > space group. However, I never came across a situation where this > was interesting." > > If the design of the toolbox is too restrictive to permit the user to > invent any closed set of operators they want - well thats the end of it. > As we say in the UK, C'est la vie. Could you please outline a plausible example where the current implementation is a serious limitation? > There were lots of things we would have liked to add to CRYSTALS, but > there was no room in Bob Carruthers database, and extending it would > have been a major hasle. I am sure the cctbx is more flexible. > As you pointed out, there are work-arounds that can be applied by a > clever crystallographer, and the less clever ones won't even try to do > anything clever. It's a self-limiting situation! Much of what crystal > enginners want could be done if Oleg lets the user create an extended > atom parameter list, and put this into a new unit cell in P1. You can create any P1 cell you want, it is totally trivial: first use e.g. xray_structure.expand_to_p1(), then loop over the translations you want to duplicate the atoms. We can easily add methods to do it in one call. Note that the cctbx is open source, with the possibility of write access to the main source repository. Cheers, Ralf ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com

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Re: [cctbxbb] Fail to extend space-group with centring translations
by Ralf W. Grosse-Kunstleve 10 Dec '06

10 Dec '06

Hi Luc, You can make both examples work like this: from cctbx.sgtbx import * info = space_group_info("P2/a") g = info.group() g.expand_ltr(tr_vec((1,1,1),2).new_denominator(sg_t_den)) from cctbx import sgtbx s = sgtbx.space_group_symbols("P21/c") g = sgtbx.space_group(s) g.expand_ltr(sgtbx.tr_vec((1,0,1),3).new_denominator(sg_t_den)) g.expand_ltr(sgtbx.tr_vec((2,0,2),3).new_denominator(sg_t_den)) Any setting of any crystallographic space group can be processed via sgtbx.space_group, as long as the rotation matrix elements are integers. You may just have to be careful in choosing appropriate "t_den" (translation denominators). All matrices in a given space_group instance have to have the same t_den. I know it can be a hassle, but I don't consider it a practical limitation. Note that sg_t_den is just the default (12). You can set other values if necessary. You cannot change the rotation denominator (fixed at 1) for the matrices processed by sgtbx.space_group. Therefore you cannot work with, e.g. the pseudo-orthorhombic C-centered setting of a hexagonal space group. However, I never came across a situation where this was interesting. It would be possible to rewrite the sgtbx based on boost::rational<int>, but it is a big project. The advantage would be more flexibility, the disadvantage a performance decrease. If there is a strong reason I would go for more flexibility, but so far I've never found this worthwhile. BTW: A more convenient way of adding symmetry operations is: g.expand_smx("x+1/2,y+1/2,z+1/2") Cheers, Ralf ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com

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Fail to extend space-group with centring translations
by Luc Bourhis 09 Dec '06

09 Dec '06

Hello there, with the latest cctbx release, the following Python snippet fails from cctbx.sgtbx import * info = space_group_info("P2/a") g = info.group() g.expand_ltr(tr_vec((1,1,1),2)) The exception indicates that it is not possible to add a centring translation with a denominator of 2 to a group which does not have any centring translations with that denominator. Of course, in that case, that description is trivial because P2/a does not have any centring translations! My real intent was actually to introduce 1/3 centring translations so as to deal with a tripled cell. I am just citing the example above to show the extent of the problem. My original, failing, snippet was therefore from cctbx import sgtbx s = sgtbx.space_group_symbols("P21/c") g = sgtbx.space_group(s) g.expand_ltr(sgtbx.tr_vec((1,0,1),3)) g.expand_ltr(sgtbx.tr_vec((2,0,2),3)) It fails with the same class of exception. It seems like it is a deeply rooted limitation and that brings me to the bigger picture. I am currently working on an EPSRC grant to write the next generation of small molecule crystallographic software, a joint collaboration between Judith Howard in Durham and David Watkin in Oxford (all in UK, just in case…!). The CCTBX is obviously a seducing foundation for such a project. Thus we have tried to push it into corners which do actually matter to a significant minority of small molecule crystallographers. So I would like to know how difficult it would be to lift the limitation at hand. Would it trigger a cascade of changes throughout the sgtbx? Luc Bourhis

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Obtaining symmetry information
by Konrad Hinsen 04 Dec '06

04 Dec '06

Dear All, I am trying to reconstruct an entire unit cell from an cctbx.xray.structure object that contains the scatterers in the asymmetric unit. Ideally, I'd call a method that does the work for me, but at least I would like to obtain a list of the symmetry transformations that must be applied. That information must be somewhere in there... but where? Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen(a)cnrs-orleans.fr ---------------------------------------------------------------------

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compiling problem with latest cctbx on OS X
by William Scott 30 Aug '06

30 Aug '06

With Ralf and Erik's help and advice, (cf http://www.phenix- online.org/pipermail/cctbxbb/2005-September/thread.html ) I made a Mac OS X fink package for the cctbx source release. http://pdb.finkproject.org/pdb/search.php?summary=cctbx Everything works fine on OS X v. 10.4, gcc 4.0.1, on both ppc and intel platforms, until today when I realized the package I made is now out of date (as of July I think). I'm now having problems compiling the latest version. I've put the log file here: http://xanana.ucsc.edu/~wgscott/kipaut/fink/compile.log Briefly, I think the failure is taking place here: c++ -o cctbx/translation_search/boost_python/fast_nv1995.o -c -fPIC - no-cpp-precomp -ftemplate-depth-130 -Wno-long-double -w - DBOOST_DISABLE_THREADS -DNDEBUG -O3 -ffast-math - DBOOST_PYTHON_MAX_BASES=2 -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/boost -Iinclude -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/include -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/cctbx/include -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/scitbx/include -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources -I/Library/Frameworks/Python.framework/Versions/2.4/ include/python2.4 /sw/src/fink.build/cctbx-60705-1001/cctbx_sources/ cctbx/translation_search/boost_python/fast_nv1995.cpp /sw/src/fink.build/cctbx-60705-1001/cctbx_sources/scitbx/include/ scitbx/fftpack/complex_to_complex.h: In member function 'void scitbx::fftpack::complex_to_complex<RealType, ComplexType>::pass3 (scitbx::fftpack::select_sign<Tag>, size_t, size_t, RealType*, RealType*, const RealType*, const RealType*)': /sw/src/fink.build/cctbx-60705-1001/cctbx_sources/scitbx/include/ scitbx/fftpack/complex_to_complex.h:361: error: expected unqualified- id before numeric constant Any suggestions? Thanks. Bill Scott

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Generate atom data from cctbx
by Jen-Chang Chen 16 Jan '06

16 Jan '06

Dear Sirs, I have installed "cctbx" in my Linux box and ran the examples,e.g. the beach in the box and the Cr2O3 case demonstrated in the mailing list, successfully. I'd like to apply cctbx as a generator of the crystallographic data. Based on the ICSD database, I can obtain a crystal structure of a mineral. Would it be possible to print out all atom positions in a unit cell or a supercell using cctbx? Thank you very much. Sincerely, Jen-Chang "James" Chen

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Re: [cctbxbb] Problems with conversion from conventional to primitive cell
by Jörg-Rüdiger Hill 25 Nov '05

25 Nov '05

Thanks for your script. I am doing this in C++. I can't find a xray::structure class in the C++ documentation. Does this only exist in Python ? Nevertheless, I run your script in Python and the result is somewhat different from what I get, but I still think it is wrong. If I create and visualize a supercell from the coordinates given by the script (e. g., with gdis) I no longer see the hexagonal arrangement of the atoms typical for the conventional cell. Since the conversion from conventional to primitive cell should only redefine the cell but not the atom positions (in Cartesian coordinates) I believe the output is incorrect. Best Regards, Jörg-Rüdiger Hill >--- J?rg-R?diger Hill <Joerg-Ruediger.Hill(a)scienomics.com> wrote: >> Dear All, >> I am trying to convert from a conventional cell to a primitive cell using >> cctbx, but I am having some problems. > >Are you doing this in C++ or in Python? > >> What I do is the following: >> 1) I construct a spaceGroup object using the space group symbol >> 2) I retrieve the change of basis operator using z2p_op() from the space >> group object >> 3) I apply this operator to the conventional cell >> 4) I take a list of symmetry unique atoms and apply the operator to their >> fractional coordinates >> At this point I have a primitive cell which agrees exactly with what I get >> from other codes. > >Note that there are ambiguities in the choice of the change-of-basis operator >to the primitive cell. You may get different results from different programs, >which are all correct. It is a coincidence if you get the same result. > >> The problem comes when I am trying to construct all atoms >> from the symmetry unique ones. I do this by the following procedure: >> 5) I take the space group object and call its change_basis() method with >> the z2p_op() operator >> 6) I loop over all order_z() symmetry operations in the space group >> applying the operation to the fractional coordinates making sure that I >> don't create two atoms at the same position > >You could use the site_symmetry and sym_equiv_sites classes to deal with the >special positions. > >> The whole procedure works well, e. g., for cubic crystals. However, if I >> take a hexagonal crystal (e. g., Cr2O3, R -3 c) the crystal build by steps >> 5 and 6 above is not correct. In this case the conventional cell has a=b != >> c, >> alpha=beta=90, and gamma=120, but the primitive cell has a=b=c and >> alpha=beta=gamma. > >That's what I'd expect. > >> I have tried to add ":R" to the space group symbol and >> constructing a new spaceGroup object in step 5 above, but that does not >> make any difference. What do I have to do to build the crystal in this case >> or what is wrong with my procedure ? > >Attached is a copy of the new cctbx/cctbx/examples/cr2o3_primitive_cell.py >script (in the CVS already; will also be in the next set of auto-build >bundles). Could you please compare your results to the output of this script? > >The script shows a high-level implementation. I could add a lower-level >equivalent that is more in line with what you'd do in C++. Let me know if > this is what you need. > >Cheers, > Ralf > > >from cctbx import xray >from cctbx import crystal >from cctbx.array_family import flex > >def demo(): > """ > Result of ICSD query: > N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000) > C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000 > S GRUP R -3 C > A Cr1 0.000000 0.000000 0.347570 0.000000 > A O1 0.305830 0.000000 0.250000 > """ > crystal_symmetry = crystal.symmetry( > unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000", > space_group_symbol="R -3 C") > scatterers = flex.xray_scatterer() > scatterers.append(xray.scatterer( > label="Cr1", site=(0.000000,0.000000,0.347570))) > scatterers.append(xray.scatterer( > label="O1", site=(0.305830,0.000000,0.250000))) > icsd_structure = xray.structure( > crystal_symmetry=crystal_symmetry, > scatterers=scatterers) > icsd_structure.show_summary().show_scatterers() > print > icsd_structure.show_distances(distance_cutoff=2.5) > print > primitive_structure = icsd_structure.primitive_setting() > primitive_structure.show_summary().show_scatterers() > print > p1_structure = primitive_structure.expand_to_p1() > p1_structure.show_summary().show_scatterers() > print > print "OK" > >if (__name__ == "__main__"): > demo() -- ------------------------------------------------------------------------------- Dr. Jörg-Rüdiger Hill Tel.: +33 1 53 43 51 05 Director R & D Tel. (direct): +49 89 613 05 700 Scienomics Fax: +33 1 53 43 92 92 17 Square Edouard VII E-Mail: Joerg-Ruediger.Hill(a)scienomics.com 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------

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Problems with conversion from conventional to primitive cell
by Jörg-Rüdiger Hill 24 Nov '05

24 Nov '05

Dear All, I am trying to convert from a conventional cell to a primitive cell using cctbx, but I am having some problems. What I do is the following: 1) I construct a spaceGroup object using the space group symbol 2) I retrieve the change of basis operator using z2p_op() from the space group object 3) I apply this operator to the conventional cell 4) I take a list of symmetry unique atoms and apply the operator to their fractional coordinates At this point I have a primitive cell which agrees exactly with what I get from other codes. The problem comes when I am trying to construct all atoms from the symmetry unique ones. I do this by the following procedure: 5) I take the space group object and call its change_basis() method with the z2p_op() operator 6) I loop over all order_z() symmetry operations in the space group applying the operation to the fractional coordinates making sure that I don't create two atoms at the same position The whole procedure works well, e. g., for cubic crystals. However, if I take a hexagonal crystal (e. g., Cr2O3, R -3 c) the crystal build by steps 5 and 6 above is not correct. In this case the conventional cell has a=b != c, alpha=beta=90, and gamma=120, but the primitive cell has a=b=c and alpha=beta=gamma. I have tried to add ":R" to the space group symbol and constructing a new spaceGroup object in step 5 above, but that does not make any difference. What do I have to do to build the crystal in this case or what is wrong with my procedure ? Best Regards, Jörg-Rüdiger Hill -- ------------------------------------------------------------------------------- Dr. Jörg-Rüdiger Hill Tel.: +33 1 53 43 51 05 Director R & D Tel. (direct): +49 89 613 05 700 Scienomics Fax: +33 1 53 43 92 92 17 Square Edouard VII E-Mail: Joerg-Ruediger.Hill(a)scienomics.com 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------

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mmtbx source tree moved to SourceForge CVS
by Ralf W. Grosse-Kunstleve 25 Oct '05

25 Oct '05

Today we've finally moved the mmtbx source tree from our private CVS server (cci.lbl.gov) to SourceForge. **** Old working copies checked out from cci.lbl.gov are no longer valid and should be removed. **** To check out a new working copy from SourceForge: Developer access: cvs [email protected]:/cvsroot/cctbx co -P mmtbx replace "user" with your SourceForge user name. Anonymous access: cvs -d:pserver:[email protected]:/cvsroot/cctbx co -P mmtbx It may take a few hours before the anonymous access is available and before the mmtbx tree is visible in the viewcvs web interface. For the records: we were hesitant to move more source trees to SourceForge because the CVS server was often heavily overloaded; a cvs update could take a significant amount of time. However, a recent hardware upgrade at SourceForge has improved performance dramatically. Performance has been very good for a couple of months. Therefore we feel it is a good opportunity to finally move the mmtbx sources to the proper place. This way, browsing the tree via viewcvs is available to everybody, and the automatic archiving of cvs activities (via email) should now work reliably for all developers. Cheers, Ralf __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

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strange silicon
by Marc Gailhanou 18 Oct '05

18 Oct '05

Hello, I have some trouble with cctbx, I try to understand why and I do not succeed. I need your help ! I replaced quartz with silicon in the "beach in the box" example/tutorial. This is the resulting code : from cctbx import xray from cctbx import crystal from cctbx.array_family import flex silicon_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.4307,5.4307,5.4307,90,90,90), space_group_symbol="Fd3m")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(0.,0.,0.), u=0) ])) silicon_structure.show_summary().show_scatterers() for scatterer in silicon_structure.scatterers(): print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site site_symmetry = silicon_structure.site_symmetry(scatterer.site) print " point group type:", site_symmetry.point_group_type() print " special position operator:", site_symmetry.special_op() f_calc = silicon_structure.structure_factors(d_min=1).f_calc() f_calc.show_summary().show_array() and running the script gives the following result result : Number of scatterers: 1 At special positions: 1 Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90) Space group: F d -3 m :2 (No. 227) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Si Si 16 ( 0.0000 0.0000 0.0000) 1.00 0.0000 Si: 0.0000 0.0000 0.0000 point group type: -3m special position operator: 0,0,0 Miller array info: None Observation type: None Type of data: complex_double, size=9 Type of sigmas: None Number of Miller indices: 9 Anomalous flag: False Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90) Space group: F d -3 m :2 (No. 227) (0, 2, 2) 0j (0, 4, 0) (120.217658126+0j) (1, 1, 1) (-84.1884955081+0j) (1, 3, 1) (65.4837172721+0j) (1, 3, 3) (57.4543830832+0j) (1, 5, 1) (-51.4875968695+0j) (2, 2, 2) (128.545406989+0j) (2, 4, 2) 0j (3, 3, 3) (-51.4875968695+0j) The 220 structure factor, at least, does not look correct . I do not understand the 16 multiplicity either. Is there something I miss ? Best regards Marc

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