- cctbxbb - phenix-online.org

iotbx newbie question
by wtempel 07 Nov '13

07 Nov '13

Hello all, please consider the scenario of a manuscript that, among other things, describes 20 crystal structures. Suppose the journal editor requires a Table 1. I now looking for a tool to prepare such table with high accuracy and little effort. My PDB deposition workflow includes the preparation of mmcif coordinates with pdb_extract. The mmcif file is complete in the sense that after upload to RCSB-ADIT, virtually no additional information is required for deposition. My intuition was to combine CSV and IOTBX python modules and produce the table via input of a list of mmcif files. The current phenix table_1 tool provides some, but not all of that functionality, and I thought once familiar with the python modules, I would quickly write the script. After confirming that the example at http://cctbx.sourceforge.net/iotbx_cif/ works with my cctbx installation, I attempted to transform that code to read in PDB mmcif coordinates: <code> test_structure = iotbx.cif.reader( file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"] </code> which throws an exception: <output> Traceback (most recent call last): File "1NXC.py", line 3, in <module> test_structure = iotbx.cif.reader(file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"] KeyError: '1NXC' </output> How do I need to write the code so that it returns a python object with access to all the cif items? Thank you, Wolfram Tempel

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compiler warning in dxtbx
by Oleg Dolomanov 04 Nov '13

04 Nov '13

Hi guys, there was big change in dxtbx/model/panel.h on the 30th of October (r18499) and apparently the != operator became recursive by calling itself rather than the == operator (line 378) - whoever is responsible - please check/fix, Cheers, Oleg.

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Request for a fix in CC1/2 calculation in phenix.merging_statistics
by Keitaro Yamashita 28 Oct '13

28 Oct '13

Dear CCTBX developers, I found a big difference in CC1/2 value (say, 77.3 vs 68.3) between phenix.merging_statistics and XSCALE when more than one *anomalous* dataset was merged in XSCALE. phenix.merging_statistics seems to assume that equivalent (in case of anomalous, here I do not consider Friedel pairs as equivalent) reflections are sorted (equivalent reflections are not separeted) in the input file. Usually, this assumption should be correct. However, if multiple anomalous datasets were merged in XSCALE, this assumption is not correct. Because Friedel pairs are not necessarily separated. This is a real example (in P43212). These lines are extracted from .HKL file by XSCALE: > 1 -41 1 1.749E+04 1.657E+05 2052.0 2467.7 78.8 -113.23 1 > 41 -1 -1 4.569E+03 6.014E+03 454.1 1112.8 132.2 116.90 1 > 41 1 -1 8.721E+03 2.637E+03 473.0 1064.4 130.4 116.11 2 > 41 1 1 7.634E+03 2.417E+03 498.2 1010.8 135.3 115.65 2 > -1 -41 -1 4.847E+03 1.997E+03 1892.9 2543.0 85.9 -122.78 2 The last number indicates the dataset the reflection belongs to. Here, (1 -41 1), (41 -1 -1), (41, 1, 1), and (-1, -41, -1) are equivalent reflections, but (41, 1, -1) in the middle is not when anomalous data! Therefore, in phenix.merging_statistics, subsets calculation for (41,1,1) is performed twice (for first two and last two). When I changed the cctbx code to sort reflections after mapping to a.s.u., CC1/2 values by phenix.merging_statistics became closer to XSCALE. In merging_stats.__init__() in iotbx/merging_statistics.py, I inserted a line > array = array.sort("packed_indices") after > array = array.customized_copy(anomalous_flag=anomalous).map_to_asu() but I think there would be more correct way to fix this unexpected behavior. Best regards, Keitaro

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correlation function for cctbx.miller.array
by Gabor Bunkoczi 24 Oct '13

24 Oct '13

Hi, I need to calculate the correlation function between two maps, both of them are stored as miller.array objects. There is a map_correlation method, which does something similar to what I want, but this calculates the total correlation coefficient, while what I need is another miller.array with amplitudes = f1*f2 and phases = p2-p1 (where f1, f2 are amplitudes and p1, p2 are phases of map1 and map2, respectively), i.e. not just the sum of these. Is this available somewhere? There is the additional complication that the hkl-list for map1 and map2 may not be fully identical, but the intersect of the two maps could be taken. Thanks, Gabor

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Scipy / cctbx core dump
by Graeme.Winter＠diamond.ac.uk 15 Oct '13

15 Oct '13

Hi Folks, Just trying to use something here which depends on scipy but it seems scipy is not playing nice with flex: from scitbx.array_family import flex import scipy.linalg A tiny and inoffensive script however... cctbx.python boom.py show_stack(1): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/blas.py(113) <module> show_stack(2): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/misc.py(5) <module> show_stack(3): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/__init__.py(147) <module> show_stack(4): /scratch/gw56/2013/OCT/15/multi-lattice/boom/boom.py(2) <module> libc backtrace (2 frames, most recent call last): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/numpy/core/multiarray.so(PyArray_API+0) [0x7fb2064c9940] /lib64/libc.so.6() [0x37b3232920] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. I did a fresh nightly build install just to be sure :o( if I export those naughty env vars I get a core dump: cctbx.python boom.py Segmentation fault (core dumped) RHEL6.4 / scipy 0.12.0 and 0.12.1 any ideas? Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Model based outlier calculation in mmtbx.scaling.outlier_rejection
by Keitaro Yamashita 08 Sep '13

08 Sep '13

Dear cctbx developers, I am interested in the implementation of model-based reflection outlier rejection. As I read the code mmtbx/scaling/outlier_rejection.py (lines 244-351), I noticed that maybe there was a discrepancy between what log_message explained and the actual code. The log_message in the code says: > Outliers are rejected on the basis of the assumption that a scaled > log likelihood differnce 2(log[P(Fobs)]-log[P(Fmode)])/Q\" is distributed > according to a Chi-square distribution (Q\" is equal to the second > derivative of the log likelihood function of the mode of the > distribution). > The outlier threshold of the p-value relates to the p-value of the > extreme value distribution of the chi-square distribution. while actual p_value is calculated for each hkl as p_value = 1 - erf(sqrt(LLG))**N, where LLG = log p(F=Fbar | Fmodel) - log p(F=Fobs | Fmodel), and N is the number of reflections. Here, Fbar is F which gives the maximum value of p(F | Fmodel). At least, Q (the second derivative of p(F=Fbar | Fmodel)) is not used in the actual calculation. Could someone please explain the meaning of the actual calculation? Why taking square-root and raising erf() result to the power of N? Thank you very much, Keitaro

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map_to_asu - get the symop used to perform mapping
by Graeme.Winter＠diamond.ac.uk 24 Jun '13

24 Jun '13

Hi All, In the progress of trying to (for reasons of my own) reproduce scale pack unmerged format files from flex arrays of Miller indices. map_to_asu is great, but it would be great to get the symop # used to perform the mapping as a result of this (it is computed somewhere in asu.h but not easily pushed out…) Has anyone done this already? I mean the getting-of-symop-which-maps bit... Thanks, Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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build problem on ubuntu 12.04
by Alastair Fyfe 11 Jun '13

11 Jun '13

Hello, is the current cctbx build (2013_02_27_0005) known to be buildable on Ubuntu ? I tried "perl cctbx_bundle.selfx" without success. After some poking about I found an exception raised in the platform.architecture() call in env_config.py/is_64bit_architecture(). Modifying the function to simply return False allowed the build to complete (log attached).This is on 12.04 with stock python 2.7.3 and the "platform.architecture()" call works as expected in a simple test. thanks, Alastair

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updated project docs
by Nathaniel Echols 05 Jun '13

05 Jun '13

FYI, I finally updated the online documentation for the first time since switching the project backend. Included in this is the corrected link for the SVN browser, which for the record is now: http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/ (I find this somewhat over-engineered, but the old URL only shows the frozen repository as of early March, so we don't have a choice.) If anyone notices broken stuff, please let me know. -Nat

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Re: [cctbxbb] building sphinx documentation
by Jan Marten Simons 19 Apr '13

19 Apr '13

Am Donnerstag 18 April 2013 19:16:00 schrieben Sie: > Hi Jan, Hi Richard, > I have attempted to build the sphinx documentation using > dox.sphinx/build_docs.sh, and this appears to have run successfully and > produced some html which shows the table of contents etc. However, I can't > seem to find the documentation for any of the significant modules, e.g. > cctbx/xray/structure.py. When I navigate to the link for the structure > module within the xray package > (dox.sphinx/_build/html/cctbx/cctbx.xray.html#structure-module), I see > nothing other than a list of all the modules within the xray package. Am I > missing something here? Have you followed the instructions given in the comments at the top of dox.sphinx/build_docs.sh? Which version of Sphinx do you use? I'm using 1.1.3 regularly and get useful documentation (I've attached the "makescript" I use to build cctbx and the sphinx documentation. If you are interested in it I can also put the output of the sphinx run on my system with current svn on webserver over here.). Has your sphinx build completed successfully or did it abort (e.g. due to out of memory* or due to other problems)? Could you also check if build/dox.sphinx/cctbx/cctbx.xray.rst has all modules listed? > As a novice to using sphinx, I don't like to add significant documentation > in sphinx style without being able to check via generating the > documentation that what I have written is correct sphinx-speak. I can totally understand this ;). Cheers and hopefully we can get this working for you as well, Jan *) For me running sphinx with all those modules selected needs about 3.3 GiB of virtual memory (RAM) and takes a few minutes to actually finish. p.s.: Sorry didn't hit "reply all".

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