- cctbxbb - phenix-online.org

problem in "space_group_type"
by Koen De Keyser 16 Apr '08

16 Apr '08

Hi, I'm currently in the process of writing some texture analysis/visualization software (XRD pole figures, EBSD) and would like to use cctbx as a basis for the crystallography calculations, as I don't want to reinvent the wheel. Development is in C++ on Windows, and trying one of the examples from the code, I end up being able to crash the program, when running: space_group_type sg_type("C 2"); This occurs using the latest release and still happens in the (unreleased) code from 13th of April, both times, I compiled the library from source, using Visual Studio 2005 and 2008. It looks to me that the problem is situated in the Hall symbol part of the space group (those structures are indicated as bad_ptr in the debugger, when crashing) The error only occurs when running in Debug mode. In Release mode, everything works fine, suggesting a memory initialization problem. I'm unable to debug the problem myself or get more details, as I can't get the library to compile with debugging information in it (Is there an easy way to do this with the Scons build system? I haven't used Scons before.) thanks, Koen De Keyser -- ir. Koen De Keyser Solid State Sciences Ghent University Krijgslaan 281, S1 9000 Gent, Belgium Tel: +32 9 264 43 54 Fax: +32 9 264 49 96 Koen.DeKeyser(a)UGent.be

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Centos rpm
by Pascal 27 Mar '08

27 Mar '08

Hi, I didn't see any rpms for centos. Do you mind if I'll make one ? Is the spec file for fedora available somewhere ? Regards, Pascal -- Pascal Parois Glasgow university http://centos.parois.net

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Re: [cctbxbb] solvent mask
by Ralf W. Grosse-Kunstleve 18 Oct '07

18 Oct '07

Hi Celine, > Thank you for all those explanation. In fact the problem for me is not > the mean of the recalculated map obtained but the range of it, which is > no longer one. Did you consider using the raw mask with the ones and zeros directly? That's the .data attribute of the bulk_solvent object. It is an integer array, but you can convert it with .data.as_double(). See also the .mask_as_xplor_map() method. The only thing the FFT back and forth does is to introduce the Ewald-sphere truncation, which leads to a smoothing of the original mask. If you want that, a quick-and-dirty approach is to copy the .structure_factors() method, rename it, then replace miller_set.unit_cell().volume() with 1.0 in the computation of scale. I think you still need to divide by the number of grid points. Use the .fft_map() of the structure factors object (miller.array) returned by your modified method to get back a map with truncation effects, but on the same scale is the original mask. > To be more clear, what I am trying to do is to "calculate" data at > different solvent contrasts from a pdb file. So I have a series of > solvent electron densities and I would like to use the complex formula F > = Fprotein in vacuum + solvent density*Fmask where Fmask are the > structure factors from an indicator function that is 1 in the solvent > region and 0 in the protein region (= my cctbx mask). That sounds exactly like what's done by the f_model class, which will refine the "solvent density" for you. I think you can also specify a value. See mmtbx/mmtbx/examples/f_model_manager.py and the Computing Commission Newsletter No. 5 (http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf). The code in the newsletter article is out of date, but the math is still accurate and examples/f_model_manager.py is the updated code. Fcalc in the newsletter formula (page 10 of the .pdf document) is your "Fprotein in vacuum". ksol is your "solvent density". You can set Uaniso and Bsol to 0 if you want. Ralf

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Re: [cctbxbb] solvent mask
by Ralf W. Grosse-Kunstleve 15 Oct '07

15 Oct '07

Hi Celine, > I have a question about solvent mask in cctbx. I generated a mask using > the mask manager. Then I am calculating the structure factors from the > mask (using mask_manager.structure_factors() ). If I am trying to redo a > map from the calculated structure factors (outside the cctbx and I hope > without any scaling), I get a map with a mean density of zero, That's because the F000 is missing. Without the F000, the mean of an FFT map will always be exactly zero. -- This is a general feature of discrete Fourier transforms. > So I wonder what is exactly this > matrix.col(fft_manager.n_real()).product() doing? That's the number of grid points in the map. The FFT introduces this as a scale factor which we are taking out. -- Again, the number of grid point issue is a general feature of discrete Fourier transforms. > And how do I generate > structure factors for a mask without any scaling? I'm guessing the scaling is not the problem, but just the absence of F000, which you can get as map_of_coeff[0]. I think it will also work if you give an array of Miller indices including (0,0,0). We could add suppress_scaling to the signature of the .structure_factors() method, but the scale is rather arbitrary anyway, so I don't think this will be very useful. Ralf

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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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