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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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Re: [cctbxbb] cbflib_ext
by Ralf W. Grosse-Kunstleve 06 Jun '07

06 Jun '07

Hi Jon, Nick Sauter is working on the cbflib extension. He told me the current version is a very incomplete prototype, but that he expects to to have a more comprehensive extension around the end of this month. We are planning to move the source code (cbflib_adaptbx) to SourceForge where it will be freely available. Ralf ----- Original Message ---- From: Jon Wright <wright(a)esrf.fr> To: cctbxbb(a)phenix-online.org Sent: Thursday, May 31, 2007 4:30:38 AM Subject: [cctbxbb] cbflib_ext Hello everypne, google has only one hit for cbflib_ext which is in marIP.py in iotbx.detectors. Any hints as to how I should find it? It does not seem to arrive in the current windows all-in download. Irrelevant perhaps, but I also had the beginnings of a swig wrapping for cbflib which is doubtless going to be incompatible with this one. Thanks, Jon ____________________________________________________________________________________ Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7

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cbflib_ext
by Jon Wright 31 May '07

31 May '07

Hello everypne, google has only one hit for cbflib_ext which is in marIP.py in iotbx.detectors. Any hints as to how I should find it? It does not seem to arrive in the current windows all-in download. Irrelevant perhaps, but I also had the beginnings of a swig wrapping for cbflib which is doubtless going to be incompatible with this one. Thanks, Jon

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Re: [cctbxbb] mask calculation using mmtbx
by Ralf W. Grosse-Kunstleve 04 Apr '07

04 Apr '07

Hi Celine, The interfaces have changed a lot since we published the example in the newsletter. An updated version is available here: http://cci.lbl.gov/~rwgk/tmp/example_bulk_solvent_mask_2007_04_03_1806.py This is only the mask calculation. The rest of the functionality is incorporated in the f_model.manager (I think it is explained a bit in newsletter No. 5). Let me know if you are still having trouble getting the example to work with the latest cctbx version. Ralf ____________________________________________________________________________________ Don't get soaked. Take a quick peek at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather

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mask calculation using mmtbx
by celine Besnard 03 Apr '07

03 Apr '07

Hi, I am trying to use the cctbx to calclate a mask given a pdb following the exemple given on a newsletter. I am using a windows version of the cctbx extracted from the bundle. But in the exemple, the mask is constructed using the masks.mask_utils function from mmtbx. But I cannot see this function in mmtbx.masks. Is there another function I can use to construct a solvent mask? Thanks for any help Celine Besnard

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