- cctbxbb - phenix-online.org

structure factor interpolation
by celine Besnard 07 Nov '08

07 Nov '08

Hi, I am looking for a function that would allow me to interpolate the structure factors values in between the reciprocal lattice points (h,k,l not integer) so that I can get the reciprocal map not of the whole crystal but of "only one" unit-cell. Is there a simple way to do that in the cctbx ? 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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postdoc position in LBNL
by Peter Zwart 20 Oct '08

20 Oct '08

Dear All, We would like to bring the following postdoctoral research position to your attention. Within Lawrence Berkeley Laboratory, we have an opening for a postdoc to work on the development of new software for the analysis of small angle X-ray scattering (SAXS) data. The availability of user friendly, robust software analysis tools for SAXS data is of growing importance as the biological community is increasingly using SAXS as a standard method to analyze complex biological systems. We are developing a new set of tools, including a software library, for SAXS data analysis. The successful candidate will have the opportunity to work with experienced software developers in the field of biophysics and interact with users and beamline staff on SAXS beamline 7.3.3 at the Advanced Light Source (ALS) in Berkeley California. Interested candidates can contact me (Peter Zwart, PHZwart(a)lbl.gov) for more details, or visit the LBL job site at: http://jobs.lbl.gov/ Sincerely, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [cctbxbb] interpreting auto generated python interface documentation
by Ralf W. Grosse-Kunstleve 28 Aug '08

28 Aug '08

> 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. It is a iotbx.pdb.hierarchy.root instance in this case, mostly referred to as "pdb_hierarchy" or just "hierarchy". Yes, for some things you have to go into the code. The best approach is to insert print statements to see what the objects are, then run the associated tests (e.g. iotbx/pdb/tst_*.py). > 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. Thanks for pointing this out. I'll look into this next week, when I'm back home. > I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python Don't hesitate to ask. You may have many questions at first, but then they'll become fewer and far in between. I'll respond more promptly after the conference trip. Ralf

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Re: [cctbxbb] input_atom_labels_list() not available in Python?
by Ralf W. Grosse-Kunstleve 26 Aug '08

26 Aug '08

Hi Hari, > input_atom_labels_list() > This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses > this function > However I dont see that in the python interface with the current version? Is that true or am I using a different build > that does not make this available in python That method is gone, indeed, ever since about April/May this year. Look for "atoms_with_labels": cd cctbx_sources libtbx.find_files -g atoms_with_labels -f Ralf P.S.: Have to run now... will look at your other email later.

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input_atom_labels_list() not available in Python?
by hari jayaram 26 Aug '08

26 Aug '08

Thanks Nathaniel.. I too was using the approach of looking at the phenix scripts to figure things out. But I was hoping that there was a "google hidden" source of documentation for the python interfaces that I was not aware of. For the present moment the c++ documentation is much more useful .After I sent the email out , I did notice the section in the manual which says.. "Most documented C++ interfaces are also available at the Python layer. Unfortunately the documentation tools available are not capable of merging the documentations. Therefore Python users need to also consult the C++ documention." On an unrelated note The Nov 2006 newsletter and the c++ and python documentation lists a function in the class iotbx.pdb.input called input_atom_labels_list() This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses this function However I dont see that in the python interface with the current version? Is that true or am I using a different build that does not make this available in python Just curious Hari On Tue, Aug 26, 2008 at 12:50 PM, Nathaniel Echols < nathaniel.echols(a)gmail.com> wrote: > Having spent the last few months trying to learn the python side of cctbx > for my own work, I recommend looking at some of the actual programs that > call these functions (e.g. the various phenix scripts, or testing scripts) > for clues on how to use them. In particular, > iotbx/pdb/tst_atom_selection.py has examples of selection caches. (I'm not > sure how exactly the "cache" class fits in, since it isn't invoked directly > in that script, but hopefully the test script has some approximation of what > you're trying to do.) I haven't found it necessary to look at the C++ code > - boost.python obscures many details anyway, and it's usually pretty obvious > to me what's going on in the python sources based on the > variable/class/function names. > The various CCP4 newsletter articles may have some useful suggestions, but > I haven't looked at these in much detail yet. > > On Tue, Aug 26, 2008 at 9:18 AM, hari jayaram <harijay(a)gmail.com> wrote: > >> 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 >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/cctbxbb >> >> > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/cctbxbb > >

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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 17 Oct '07

17 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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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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