- cctbxbb - phenix-online.org

Re: [cctbxbb] constrained hydrogen geometry
by Ralf W. Grosse-Kunstleve 14 Dec '06

14 Dec '06

Hi Luc, > I have not been able to find any facility to constraint hydrogen > geometry, in the manner of the AFIX in ShelXL I mean. Have I missed > them or would it need to be implemented? They need to be implemented. > In the latter case, I have tried to figure out how this could be > done. I manage to find how position and ADP constraints are handled > by constraint objects featuring methods to return the independent > variables and the gradient with respect to them. Then cctbx/cctbx/ > examples/structure_factor_derivatives_4.py shows how those features > can be used. Would Hydrogen geometry constraint be best handled by > mimicking those special positions constraint? I am not sure. The handling of hydrogens seems more complicated than dealing with the constraints due to symmetry. I just had a quick look at the SHELX manual. I see many special cases. If I had a chance to work on this, I'd start with a Python script emulating some of the cases handled by SHELX, refining a few small structures. After getting a few concrete examples to work, I'd try to generalize the procedures for handling the special cases. I'd switch to C++ only after having fully conquered the math and the bookkeeping in Python, and being sure about the final interfaces. To implement the core refinement, I'd copy and modify cctbx/cctbx/xray/minimization.py. See also phenix/phenix/substructure/hyss/minimization.py, which you can find in the CCI Apps bundle (http://phenix-online.org/download/cci_apps/). Hope this helps. As you can tell, I am not an expert in constrained hydrogen refinement, but I'm very interested in seeing such algorithms in the cctbx (we'd probably want to use them in phenix.refine). Let me know if you feel I can do something to help out. Cheers, Ralf ____________________________________________________________________________________ Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com

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constrained hydrogen geometry
by Luc Bourhis 14 Dec '06

14 Dec '06

I have not been able to find any facility to constraint hydrogen geometry, in the manner of the AFIX in ShelXL I mean. Have I missed them or would it need to be implemented? In the latter case, I have tried to figure out how this could be done. I manage to find how position and ADP constraints are handled by constraint objects featuring methods to return the independent variables and the gradient with respect to them. Then cctbx/cctbx/ examples/structure_factor_derivatives_4.py shows how those features can be used. Would Hydrogen geometry constraint be best handled by mimicking those special positions constraint? Cheers, luc

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

11 Dec '06

> I believe Ralph can handle C-1 Yes, most definitely. There are no rational rotation matrix elements => no problem. > In each pair of tables 4 & 5 and 6 & 7 atomic parameters can be > compared directly. If the P to C transformation is made, all four > tables can be compared by inspection. I believe you can always achieve this even with the cctbx as is. You just may have to transform both structures to some unusual setting. Consider that matrices with rational rotation parts elements are not only relatively expensive to handle, but the corresponding geometry is also highly non-intuitive. I.e. if you transform both structures to avoid the rational rotation parts I bet the comparison is easier to explain and understand. The usual trick is to use space_group_type to go to reference settings, then .niggli_cell() to go to primitive settings, then deal with the extra translations in the primitive settings. Technically it comes down to combining the change-of-basis matrices in the right way, which is easy. > In this case, the referees and editors refused to accept a non standard > SG, so the text of the paper becomes laborious, explaining what would > otherwise have been obvious. If you give change-of-basis matrices from the reference setting (using space_group_type) I think it should be easy to argue the case for presenting the comparison using a convenient frame of reference. Note that the space_group_type has a ".universal_hermann_mauguin_symbol()" method to produce "nice" general space group symbols for any setting that can be handled by the space_group class. We use this in the automatic generation of subgroup graphs. E.g. try this: iotbx.explore_metric_symmetry --unit-cell "68.4 68.4 68.3 109.5 109.4 109.5" --space-group=p1 --graph graph.png For this to work you need graphviz (open source). If you don't have it, here is the resulting png file: http://cci.lbl.gov/~rwgk/tmp/explore_metric_symmetry_graph.png > In higer symmetry SGs it may be easier to compare structures if even more > bizzare SG are invented, or if non-standard origins are used. I don't think it is a problem if you use the right existing tools. :) > Im sure this will be true, and that someone will provide the > user-interface for generating the basis vectors form the new (probably > enlarged) cell and new atomic parameters after the expansion. I'd be happy to help integrate the required additions. > Im sure the SM-tbx folk have more pressing problems to deal with than > worrying about this minority application The core "cctbx" (the module, not the project, see Comp. Comm. Newsletter No. 1) is meant to be a small-molecule toolbox. Please don't view it as "read only", unless you don't want to release your additions as open source. (?) 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 11 Dec '06

11 Dec '06

Hi Luc, > If I understand correctly, space_group_type lets the user use any > space-group in a non-standard setting defined by a special change of > basis. space_group_type determines the change-of-basis matrix from a given setting to the reference setting. > Now your example would require the matrix of change of basis > to be rational whereas in the current implementation it can only be > integral. The change_of_basis_op class has both rational rotation and rational translation parts, with a common r_den for the 9 rotation matrix elements, and a common t_den for the 3 translation vector elements. The "r_den" is fixed at 1 only for the space_group class. Since space_group_type operates only on space_group objects, the limitation applies here too, but the resulting change-of-basis rotation parts certainly don't have to be integral (that would be a terrible limitation). > At least as far as I understand, from the code and your > comments. Thus, the only place where rational numbers would be > necessary is in those matrices of change of basis, isn't it? Now, > would it be possible to define a new class > space_group_irrational_setting which would provide services very > similar to space_group_type but accepting non-integral matrices for > the change of basis? You are correct. If you need to handle space groups with rational rotation matrices, the way forward is to implement a new class similar to space_group (I'd go for space_group_rational) with a little bit of cut-and-paste to replicate the group multiplication. However, I don't think it is worth redoing the entire space_group_type implementation to accommodate rational rotation parts. In fact, I think it would be a bad solution because of the runtime impact. Consider that any space group when transformed to the primitive setting will have only integral rotation matrices. I.e. all you need is an algorithm that figures out an "initial" change-of-basis matrix to a (any) primitive setting. Construct a standard space_group object with the transformed symmetry operations and feed it into space_group_type. Multiply the "initial" change-of-basis with the output of space_group_type, done. This way you get the desired generality with a moderate effort, without impacting the performance of the many established algorithms based on space_group. Cheers, Ralf ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited

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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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