- cctbxbb - phenix-online.org

interpreting auto generated python interface documentation
by hari jayaram 26 Aug '08

26 Aug '08

Hi , I am a few days into learning to use the cctbx libraries. My interests are mostly to be able to write scripts that plot various statistics from mtz files and use things like iotbx.pdb to manipulate coordinate files. While I have managed to write a few scripts and have read the very descriptive examples in the newsletters and the few routines inside of phenix.I have a problem with getting much out of the python interface documentation at the sourceforge site. Say , for a particular class say http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html, the documentation gives me a "cache" class __init__ method that says __init__(self, root, wildcard_escape_char=r'\') How do I find out what "root" is in this example. Should I be looking at the c++ code to find out the "types" of these arguments. In addition a few of the auto-generated documentation pages such as http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html return an error page. I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python Thanks in advance hari

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Re: [cctbxbb] getting resolution for any "h" "k" "l" and cctbx
by Ralf W. Grosse-Kunstleve 05 Aug '08

05 Aug '08

Hi Hari, > 1) I was wondering if someone can point me to routines available from > cctbx modules that can give me the "resolution" for a given index "h" > "k" "l". in any space group To get the resolution for a given hkl, you just need the unit cell: from cctbx import uctbx uc = uctbx.unit_cell((11,12,13,93,98,103)) hkl = (2,3,4) print uc.d(miller_index=hkl) print uc.stol(miller_index=hkl) wavelength = 1.3 print uc.two_theta(miller_index=hkl, wavelength=wavelength) Save as "resolution_hkl.py" and run with: cctbx.python resolution_hkl.py The .d(), .stol(), .two_theta() methods are documented here: http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1uni… > 2) In addition , if someone can point me in the direction of a well > illustrated depiction of the derivation of the reciprocal lattice > for the triclinic case , that will be very much appreciated bonus . I'm not sure which textbook to recommend. I liked the old Buerger books a lot, but I don't remember how he introduces the reciprocal lattice. Ralf

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getting resolution for any "h" "k" "l" and cctbx
by hari jayaram 05 Aug '08

05 Aug '08

Hi , I have been programming in python for a little bit, I am new to cctbx . My crystallography knowledge is as good as solving a few structures gives you. I have a few questions. 1) I was wondering if someone can point me to routines available from cctbx modules that can give me the "resolution" for a given index "h" "k" "l". in any space group 2) In addition , if someone can point me in the direction of a well illustrated depiction of the derivation of the reciprocal lattice for the triclinic case , that will be very much appreciated bonus . Thank you in advance Hari

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Re: [cctbxbb] (no subject)
by Ralf W. Grosse-Kunstleve 26 May '08

26 May '08

Hi Xie, > Are cctbx and phenix compatible with a 64 bit operating system? Yes. > I have Ubuntu 8.04 (64 bit) installed on an Intel Core2 duo system. Please try the source bundle: cctbx_python_252_bundle.selfx http://cci.lbl.gov/cctbx_build/ Let me know if there are any problems. Ralf

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(no subject)
by Xie Jiabao 26 May '08

26 May '08

Hi, Are cctbx and phenix compatible with a 64 bit operating system? I have Ubuntu 8.04 (64 bit) installed on an Intel Core2 duo system. Thanks, Xie

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Re: [cctbxbb] problem in "space_group_type"
by Ralf W. Grosse-Kunstleve 16 Apr '08

16 Apr '08

Hi Koen, > The error only occurs when running in Debug mode. In Release mode, > everything works fine, suggesting a memory initialization problem. This is a known feature of Windows: libraries compiled in release and debug mode are not binary compatible. Under Linux I check with valgrind all the time, therefore it is almost certain that the Windows debug/release mix is the only 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.) The *one* script to change is libtbx/SConscript Currently, in the if (sys.platform == "win32"): ... if (env_etc.compiler == "win32_cl"): branch you'll find: if (libtbx.env.build_options.debug_symbols): raise RuntimeError("Debug build not supported.") This is the place to start. On Unix platforms it simply works like this: if (libtbx.env.build_options.debug_symbols): opts.insert(0, "-g") I forgot the details of why it is more complicated under Windows. I vaguely recall that there were issues linking with the correct runtime libraries, in particular linking with the correct Python runtime. Idea: replace the RuntimeError above with opts.insert(0, "???") and initialize a new build directory with libtbx\configure.py --build-boost-python-extensions=False --build=debug Since you are not building Python extensions, the Python runtime library problem goes away. Ralf

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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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