- cctbxbb - phenix-online.org

cctbx now available on conda-forge
by Billy Poon 23 Sep '20

23 Sep '20

Hi everyone, The conda-forge package for cctbx is now available. There are 2 packages, "cctbx-base" includes the base code and "cctbx" which includes "cctbx-base" and adds "wxPython", "PySide2", and "ipython". The commands for installing cctbx into your conda environment are conda install -c conda-forge cctbx or conda install -c conda-forge cctbx-base If you want to use Jupyter Lab, you can now easily do this with conda install -c conda-forge cctbx-base jupyterlab jupyter lab The existing documentation will be updated to reflect the easier installation procedure with conda. After installing the conda package, you can also run some of the tests (in an empty directory) with libtbx.run_tests_module module=libtbx module=cctbx nproc=<nproc> I do know of a few issues that I want to fix in upcoming releases, but please submit issues to https://github.com/cctbx/cctbx_project with steps to reproduce the error. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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E value calculation
by Academic Research 03 Sep '20

03 Sep '20

Hello Everyone, I am trying to find how to perform the E value calculation using CCTBX. I am unable to find the method in the documentation. Can someone assist me, please? Regards, AC Research

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Changes to boost_adaptbx and
by Billy Poon 18 Aug '20

18 Aug '20

Hi everyone, Two pull requests were merged today that make some important changes. 1) The boost imports were moved to boost_adaptbx.boost. This avoids claiming the main "boost" namespace. A common piece of code that will need to be changed is import boost.python ext = boost.python.import_ext("your_boost_python_ext") That can be changed to import boost_adaptbx.boost.python as bp ext = bp.import_ext("your_boost_python_ext") Otherwise, a FutureWarning will be raised. More information can be found at https://github.com/cctbx/cctbx_project/issues/458 https://github.com/cctbx/cctbx_project/pull/470 https://github.com/cctbx/cctbx_project/pull/516 2) More dependency repositories were moved from cci.lbl.gov to GitHub. If you use bootstrap.py to build cctbx, you will want to delete annlib, ccp4io_adaptbx, clipper, eigen, gui_resources, tntbx. Using a newly updated bootstrap.py, the copies from GitHub will be used instead. More information can be found at https://github.com/cctbx/cctbx_project/pull/408 Let us know if you have any questions. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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unmerged data as mtz object
by Robert Oeffner 04 Aug '20

04 Aug '20

Hi, Does anybody know how to convert a miller array of unmerged data to an mtz object? For merged data I do something like this: mtzobj = millarr.as_mtz_dataset(column_root_label="I") But if millarr contains multiple observations with the same hkl index. Then the above code fails with the exception cctbx Error: Duplicate entries in miller_indices array. Any suggestions? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus The Keith Peters Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 -- This email has been checked for viruses by AVG. https://www.avg.com

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flex.histogram giving ArgumentError when arguments correct
by Winter, Graeme (DLSLtd,RAL,LSCI) 04 Aug '20

04 Aug '20

H = flex.histogram(coords, data_min=0.0, data_max=dim, n_slots=dim) Gives Boost.Python.ArgumentError: Please report this error to dials-support(a)lists.sourceforge.net: Python argument types in histogram.__init__(histogram) did not match C++ signature: __init__(_object*, double, double, double, scitbx::af::shared<long>, unsigned long) __init__(_object*, scitbx::histogram<double, long> other, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, double relative_tolerance=0.0001) __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, double data_min, double data_max, unsigned long n_slots=1000, double relative_tolerance=0.0001) __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, unsigned long n_slots=1000) Despite coords being <scitbx_array_family_flex_ext.double object at 0x7fa8d671b5b0> with shape (31294944,) and dim being 18093576 (i.e. integer) and h = flex.histogram(a, data_min=0, data_max=100, n_slots=100) working fine in another context i.e. the calling convention is correct This has so far cost a few hours, so what gives? How can this be holding it wrong? C++ code suggests that the bin types are long so this should be fine Any hints? 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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Python development platform
by Winter, Graeme (DLSLtd,RAL,LSCI) 18 Jul '20

18 Jul '20

Hi Folks, Came up in conversation earlier - what version of Python are people using for their day-to-day development? For what it’s worth I’m currently on a 3.6 base, though wondering about moving to e.g. 3.8 Cheers 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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How to extract I(+) and I(-) from miller array?
by Mooers, Blaine H.M. (HSC) 09 Jun '20

09 Jun '20

Hi Pavel, Thank you very much for the leads. They were very helpful. I was able to make the desired plot. Best regards, Blaine ________________________________________ From: Pavel Afonine [pafonine(a)lbl.gov] Sent: Tuesday, June 09, 2020 2:07 PM To: Mooers, Blaine H.M. (HSC); cctbx mailing list Subject: [EXTERNAL] Re: [cctbxbb] How to extract I(+) and I(-) from miller array? Hi Blaine, this is correct, this is how anomalous data are read in and stored in an instance of miller.array class. In this case I(+) and I(-) will be stored in one miller_array, anomalous_flag will be set to True, and .indices() will contain 'plus' and 'minus' mates as well as singletons. Now, if you want to get separate I(+) and I(-), for an example look in def anomalous_signal(self, use_binning=False): def anomalous_differences(self, enforce_positive_sigmas=False): def hemisphere_acentrics(self, plus_or_minus): def hemispheres_acentrics(self): def convert_to_non_anomalous_if_ratio_pairs_lone_less_than(self, threshold): in cctbx/miller/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit… . Pavel On 6/9/20 07:55, Mooers, Blaine H.M. (HSC) wrote: > Dear CCTBX experts, > > The diffraction data for 3hz7 from RC Researcher's question includes one dataset with column labels of 'I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)'. > When the diffraction data of 3hz7 data are read from a mtz file into miller arrays, > it would appear that the I(+) and I(-) are stored in a single column of intensities rather than two parallel columns. > > from iotbx.reflection_file_reader import any_reflection_file > > hkl_file = any_reflection_file('3hz7.mtz') > miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False) > Iobs = miller_arrays[1] > list(Iobs[100:105]) > > [((7, 4, 38), 84.0, 52.20000076293945), > ((-7, -4, -38), 112.80000305175781, 48.20000076293945), > ((8, 4, 38), 119.69999694824219, 57.400001525878906), > ((-8, -4, -38), 152.10000610351562, 65.9000015258789), > ((6, 5, 38), 732.5, 57.5)] > > How would I extract the I(+) and I(-) into lists to plot against each other in a scatter plot in matplotlib? > > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Molecular Biology > College of Medicine > University of Oklahoma Health Sciences Center > S.L. Young Biomedical Research Center (BRC) Rm. 466 > 975 NE 10th Street, BRC 466 > Oklahoma City, OK 73104-5419 > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai…

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How to extract I(+) and I(-) from miller array?
by Mooers, Blaine H.M. (HSC) 09 Jun '20

09 Jun '20

Dear CCTBX experts, The diffraction data for 3hz7 from RC Researcher's question includes one dataset with column labels of 'I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)'. When the diffraction data of 3hz7 data are read from a mtz file into miller arrays, it would appear that the I(+) and I(-) are stored in a single column of intensities rather than two parallel columns. from iotbx.reflection_file_reader import any_reflection_file hkl_file = any_reflection_file('3hz7.mtz') miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False) Iobs = miller_arrays[1] list(Iobs[100:105]) [((7, 4, 38), 84.0, 52.20000076293945), ((-7, -4, -38), 112.80000305175781, 48.20000076293945), ((8, 4, 38), 119.69999694824219, 57.400001525878906), ((-8, -4, -38), 152.10000610351562, 65.9000015258789), ((6, 5, 38), 732.5, 57.5)] How would I extract the I(+) and I(-) into lists to plot against each other in a scatter plot in matplotlib? Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419

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F_obs values
by Mooers, Blaine H.M. (HSC) 08 Jun '20

08 Jun '20

Dear AC Researh, To follow Pavel's suggestion, print your miller arrays, get their length, and then loop over the arrays and print the column labels. len(miller_arrays) # which returns 2 for your example. [print("Miller array %s: %s" % (i, miller_array.info().labels)) for i, miller_array in list(enumerate(miller_arrays))[:2]] Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular BiologyUniversity of Oklahoma Health Sciences Center Oklahoma City, OK 73104-5419 ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Monday, June 08, 2020 2:00 PM To: cctbxbb(a)phenix-online.org Subject: [EXTERNAL] cctbxbb Digest, Vol 135, Issue 1 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. F_obs values (Academic Research) 2. Re: F_obs values (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Sun, 07 Jun 2020 21:34:50 -0000 From: Academic Research <ac.research(a)icloud.com> To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] F_obs values Message-ID: <9b1bc3ab-2421-4faa-b6f4-fd1ecd63415a(a)me.com> Content-Type: text/plain; charset="utf-8"; Format="flowed" Hello Everyone, I am trying to follow the script on the CCTBX website to get the F_obs values for my 3hz7.mtz file. my code is as follows: from iotbx.reflection_file_reader import any_reflection_file hkl_file = any_reflection_file('3hz7.mtz') arrays = hkl_file.as_miller_arrays(merge_equivalents=False) a = arrays[0] f_obs = a.f_sq_as_f().map_to_asu() I get this following error: Traceback (most recent call last): ? File "https://urldefense.proofpoint.com/v2/url?u=http-3A__crystal.py&d=DwICAg&c=V… ", line 143, in <module> ??? if __name__ == '__main__': main() ? File "https://urldefense.proofpoint.com/v2/url?u=http-3A__crystal.py&d=DwICAg&c=V… ", line 140, in main ??? Cls.features('3hz7.mtz') ? File "https://urldefense.proofpoint.com/v2/url?u=http-3A__crystal.py&d=DwICAg&c=V… ", line 63, in features ??? f_obs = a.f_sq_as_f().map_to_asu() ? File "/home/acresearch/Desktop/CCTBX/mc3/envs/tenv/lib/python3.8/site-packages/cctbx/miller/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=oAfuCKnHEMReNwNf8K-J-MEXUEuhmfZEy8PYiJVy68I&s=LeX7G1Xgo9XI-pi0Su5OxLY6PfDhKilIfshCkSXXcPU&e= ", line 2374, in f_sq_as_f ??? result = array(self, converter(self.data()).f) Boost.Python.ArgumentError: Python argument types in ??? array_f_sq_as_f_xtal_3_7.__init__(array_f_sq_as_f_xtal_3_7, int) did not match C++ signature: ??? __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>) ??? __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>) ??? __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>, double) When I run: print(i_obs.info()) I get: 3hz7.mtz:FREE print(a.observation_type()) gives: None I repeated this script to many structure from the PDB (all solved by x-rays) yet I get the exact same output for all of them. How can I get the F_obs values? Can someone please assist me? Regards, AC Research

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F_obs values
by Academic Research 07 Jun '20

07 Jun '20

Hello Everyone, I am trying to follow the script on the CCTBX website to get the F_obs values for my 3hz7.mtz file. my code is as follows: from iotbx.reflection_file_reader import any_reflection_file hkl_file = any_reflection_file('3hz7.mtz') arrays = hkl_file.as_miller_arrays(merge_equivalents=False) a = arrays[0] f_obs = a.f_sq_as_f().map_to_asu() I get this following error: Traceback (most recent call last): File "crystal.py", line 143, in <module> if __name__ == '__main__': main() File "crystal.py", line 140, in main Cls.features('3hz7.mtz') File "crystal.py", line 63, in features f_obs = a.f_sq_as_f().map_to_asu() File "/home/acresearch/Desktop/CCTBX/mc3/envs/tenv/lib/python3.8/site-packages/cctbx/miller/__init__.py", line 2374, in f_sq_as_f result = array(self, converter(self.data()).f) Boost.Python.ArgumentError: Python argument types in array_f_sq_as_f_xtal_3_7.__init__(array_f_sq_as_f_xtal_3_7, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>) __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>) __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>, scitbx::af::const_ref<double, scitbx::af::trivial_accessor>, double) When I run: print(i_obs.info()) I get: 3hz7.mtz:FREE print(a.observation_type()) gives: None I repeated this script to many structure from the PDB (all solved by x-rays) yet I get the exact same output for all of them. How can I get the F_obs values? Can someone please assist me? Regards, AC Research

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