- cctbxbb - phenix-online.org

coordinates -> space group + matrices
by Kris Andersen 15 Oct '07

15 Oct '07

This is probably a simple (maybe stupid) question, but that never stopped me before: I want to give cctbx a set of primitive vectors and coordinates (cartesian or fractional), and have it return (1) the space group and (2) all the symmetry matrices. For example, given R = [4 0 0 % primitive vectors 0 4 0 0 0 4] x = [0.00 0.0 0.00 % fractional coordinates 0.51 0.51 0.51 0.50 0.50 0.00 0.00 0.50 0.50 0.50 0.00 0.50] I want cctbx to tell me this is space group #160 R3m, that there are 6 symmetry operations, and give me the corresponding matrices. This sounds easy, given everything cctbx can do, so it must be possible. Is there a simple example anywhere? Thanks. -- Kristopher E. Andersen http://www.physics.nau.edu/~andersen/ Northern Arizona University kris.andersen(a)nau.edu Department of Physics and Astronomy (928) 523-7202

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Re: [cctbxbb] coordinates -> space group + matrices
by Ralf W. Grosse-Kunstleve 18 Sep '07

18 Sep '07

Hi Kris, your questions isn't simple and the solution isn't straightforward. The functionality you are looking for isn't implemented in the cctbx. You are right in your assumption that most of what you need is already available, but there are missing pieces. Given a unit cell (your primitive vectors), the cctbx can give you the corresponding highest point-group symmetry (lattice symmetry) in a very robust way, but there is nothing to loop over the compatible space groups and to check if the symmetry operations are compatible with the coordinates. There are some programs out there which do this. I think Ton Spek's PLATON for example. The Superflip program (google) determines the symmetry from a P1 map. There is also J. Appl. Cryst. (2005). 38, 237-238 and J. Appl. Cryst. (1998). 31, 922-928. There may be more. I haven't followed the developments very closely. An idea that has been floating around in my mind for a long time is to use the fast translation function. Make a map given your coordinates, loop over all space group, use the fast translation function to find the origin. This is implemented in phenix.hyss. It should be relatively easy to adapt this implementation for your purpose. You'd get scores (correlation coefficients) instead of yes/no answers. This could be useful to uncover approximate symmetry, but I'm just guessing. If you want to try implementations yourself, I'd be happy to answer specific questions. Ralf ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469

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Re: [cctbxbb] structure_factors_from_map
by Ralf W. Grosse-Kunstleve 09 Jul '07

09 Jul '07

Hi Philipp, The two FFTs introduce a scale factor equivalent to the number of grid points. Please try adding this code: x = abs(new_array).data() y = abs(very_new_array).data() lc = flex.linear_correlation(x, y) lc.show_summary() lr = flex.linear_regression(x, y) lr.show_summary() The correlation coefficient should be 1.0 exactly, and the linear-regression slope is the same as the "total number of grid points" shown in the output: total number of grid points: 345600 ... is_well_defined: True mean_x: 43.9292797741 mean_y: 15181959.0899 coefficient: 1.0 is_well_defined: True y_intercept: 5.1687812285e-07 slope: 345600.0 Ralf ____________________________________________________________________________________Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/

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Re: [cctbxbb] pdb output
by Ralf W. Grosse-Kunstleve 09 Jul '07

09 Jul '07

Hi Celine, There isn't something like a pdb.output object, but there are a few helper functions for writing certain records. E.g. see section 5.6 of this newsletter: http://cci.lbl.gov/publications/download/iucrcompcomm_nov2006.pdf Look for "def format_" in iotbx/iotbx/pdb/__init__.py. Ralf ----- Original Message ---- From: celine Besnard <celine.besnard(a)epfl.ch> To: cctbxbb(a)phenix-online.org Sent: Monday, July 9, 2007 9:02:05 AM Subject: [cctbxbb] pdb output Hello I have a structure object which I want to write a pdb file from. Is there any function that does the contrary of the pdb.input function in the iotbx? I have not been able to find one. Thanks Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/cctbxbb ____________________________________________________________________________________ Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091

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pdb output
by celine Besnard 09 Jul '07

09 Jul '07

Hello I have a structure object which I want to write a pdb file from. Is there any function that does the contrary of the pdb.input function in the iotbx? I have not been able to find one. Thanks Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch

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structure_factors_from_map
by Philipp Heuser 09 Jul '07

09 Jul '07

Hi, thanks for the help with my asymmetric unit problem again. However I do have further questions further down my pipeline regarding the backwards fft from the map to structure factors: Am I right if I assume that fft_map = new_array.fft_map(resolution_factor=1/3., symmetry_flags=maptbx.use_space_group_symmetry) real_map = fft_map.real_map() very_new_array=new_array.structure_factors_from_map(map=real_map) #Output1 new_array.show_array() #Output2 very_new_array.show_array() Output1 and Output2 should be identical? They are not... Do I have to consider something, so that they are identical? Thanks and kind regards Philipp -- -------------------------------------------------- Dr Philipp Heuser Postdoctoral fellow EMBL-Hamburg c/o Building 25A, DESY Notkestrasse 85 22603 Hamburg phone: +49 40 89902 188 fax: +49 40 89902 149 mail: philipp.heuser(a)embl-hamburg.de web: www.philipp-heuser.de --------------------------------------------------

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Re: [cctbxbb] Asymmetric Unit with cctbx
by Ralf W. Grosse-Kunstleve 25 Jun '07

25 Jun '07

Hi Phillip, Could you give a brief overview of what you want to do? There are many ways of handling the contiguous asu information, but how much effort a particular approach is worth highly depends on the application. E.g. it is important to understand how important runtime performance is vs. memory use vs. developer time. Note that the contiguous asymmetric units are fully defined in the cctbx.sgtbx.direct_space_asu module (this is behind the asu gallery Peter pointed out). However, the full information for handling all conditions on the facets, edges and vertices is only available in Python. For processing maps this is likely to be too slow, unless you really don't care about runtime. In C++, the contiguous asymmetric units are only used as volumes: cctbx/crystal/direct_space_asu.h, classes float_cut_plane and float_asu, which duplicate some of the Python code. It is not a severe duplication since the facet/edge/vertex conditions are meaningless when working with floating-point numbers and can therefore be dropped. When dealing with grid points in maps you need those conditions somehow, either from some sort of reference table as we have in Python, or by looping over the symmetry operations. Handling the full conditions in C++ would be quite a bit of work, I think. It would be cool to have in general, but so far I didn't have an application important enough to justify the effort. Ralf ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097

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Re: [cctbxbb] Asymmetric Unit with cctbx
by Ralf W. Grosse-Kunstleve 22 Jun '07

22 Jun '07

Hi Phillip, sorry, that was an oversight. Replace - real_map = fft_map.real_map() + real_map = fft_map.real_map_unpadded() and it should print identical values. > Is there any reason for the different sizes of the tag_array and the > real_map? real_map.last() and tag_array.last() show different results. That was exactly the problem. The real_map is padded because of FFT requirements. The tag_array is not. .real_map_unpadded() will make a copy. There will be another copy to restore the padding in .structure_factors_from_map() call. The two copies can be avoided in C++, but it is to cumbersome from Python. Ralf ____________________________________________________________________________________ Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/

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Re: [cctbxbb] Asymmetric Unit with cctbx
by Ralf W. Grosse-Kunstleve 20 Jun '07

20 Jun '07

Hi Philipp, You can find an expanded version of your script here: http://cci.lbl.gov/~rwgk/tmp/cctbx_examples/2007_06_17/ Use this command to generate a fake mtz file: iotbx.python random_f_calc.py P31 Then this command: iotbx.python mtz_to_map_and_back.py random_f_calcs.mtz FC1 FC2 This illustrates how to convert a manipulated map back to Fourier coefficients (via .structure_factors_from_map()) and write these out in MTZ format. In the example, the map manipulation is simply squaring the map. You can do anything else with the map from Python. For the FFT back to Fourier coefficients, you need a map over the unit cell. For maps, we don't have continuous asymmetric units (the map code pre-dates the ASU gallery). Instead, we have a "tag array" of integer values with the same gridding as the data map. An integer value less than 0 means "this grid point is unique under symmetry", values >= 0 are the 1D indices of the symmetry-related unique point. See the code near the end of mtz_to_map_and_back.py. It shows a loop over the grid points accessing both the tag_array and the real_map. This loop is slow, of course, since it is in Python. It should be fast enough for prototyping, but I'd expect the final version to be implemented in C++, unless your manipulation can be formulated with existing array algebra, e.g. the flex.pow2() in the example, which already runs at C++ speed. Cheers, Ralf ____________________________________________________________________________________ Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC

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Asymmetric Unit with cctbx
by Philipp Heuser 15 Jun '07

15 Jun '07

Dear all! I am not sure if this is the correct place to ask beginner-questions, how to use cctbx, but I try anyway. I would like to read in a mtz file, and convert it to a density map, which I can modify in real space using the asymmetric unit, and afterwards I would like to convert my modified map back to an mtz file. Currently I am stuck at the point, where I want to reduce the map from the unit cell to the asymmetric unit. from iotbx import mtz from cctbx import miller mtz_filename="./some_mtz_file.mtz" mtz_file = mtz.object(mtz_filename) Miller_array = mtz_file.as_miller_arrays() NEW_ARRAY=Miller_array[0].phase_transfer(Miller_array[1], deg=True) #by the way: what can I do with the mandatory_factors flag? Does grid_step=1 means the grid as a 1A spacing? FFT_map = NEW_ARRAY.fft_map(grid_step=1) Real_map = FFT_map.real_map() I would be happy, if anybody could give me some advice how to do that using the cctbx libaries! Thanks in advance Regards Philipp -- -------------------------------------------------- Dr Philipp Heuser Postdoctoral fellow EMBL-Hamburg c/o Building 25A, DESY Notkestrasse 85 22603 Hamburg phone: +49 40 89902 188 fax: +49 40 89902 149 mail: philipp.heuser(a)embl-hamburg.de --------------------------------------------------

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