- cctbxbb - phenix-online.org

F_obs values
by Academic Research 08 Jun '20

08 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

2 1

Boost 1.70 update for cctbx
by Billy Poon 09 May '20

09 May '20

Hi everyone, There is currently a pull request for cctbx that will update Boost to 1.70 ( https://github.com/cctbx/cctbx_project/pull/409). The update enables support for Python 3.7 and 3.8. The plan is to merge this next Friday, May 8, at 3 pm Pacific. After merging, developers should delete the build/lib/*boost* files and build/boost directory so that any remnants of the old Boost are removed and then rebuild. Let me 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

1 1

Question about HHpred parser
by Louis Dumas 24 Apr '20

24 Apr '20

Dear CCTBX developers, I am a postdoc at EPFL working with HHpred for homology modeling of membrane proteins. I have been trying to write my own HHpred alignment parser until I found the python script under “cctbx_fork/iotbx/bioinformatics/__init__.py/” that contains an HHpred parser. My goal is to correctly parse the raw HHpred output file (.hhr), which involves unwrapping every alignment, parsing out a lot of text to finally obtain something like this: >pdb_name query-sequence column score Example: >4U15 VYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWS +........+..+..++|+++|++++.++.+.++++ +..+.++.+|+++|++.++...+........ +...|.. Being somewhat new to python, I was wondering whether the people who wrote this script are still around and could help me figure out whether the parser could be implemented in such a way. Thanks for any help you can provide! Best, Louis D

2 1

Find special positions for a spacegroup in sgtbx
by Collins, Steve (DLSLtd,RAL,SCI) 23 Mar '20

23 Mar '20

Hello, I'm trying to find something I can run from Python to get all the special (high-symmetry) positions and usual (e.g. Wyckoff) labels for a particular space group. I can't find this in the sgtbx documentation. Does anyone know if it can be done? Or maybe a different package? Thanks - and stay safe! Steve Collins -- 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

5 6

New cctbx conda packages for testing
by Billy Poon 21 Mar '20

21 Mar '20

Hi everyone, Sorry for the long delay, the current Phenix release and helping out with an experiment at SACLA earlier in the year, took priority. But I have been able to clean up the cctbx conda packages that I built at the end of last year. The major differences are as follows. 1) Windows packages are available for Python 2.7, 3.6, and 3.7. It's not clear why conda-build is having issues with Python 3.8, so I'm still sorting it out. 2) The full repositories are copied now. As a consequence, you'll be able to run some tests like "libtbx.run_tests_parallel module=cctbx nproc=24" and all the tests will run. 3) The LIBTBX_BUILD environment variable is no longer needed, so it is not set on activation of the conda environment. 4) The libtbx.configure and libtbx.refresh commands are removed from the conda package until the ability to configure/build against the conda installation of cctbx is available. Currently, those commands will break the environment. The linux and macOS packages support Python 2.7, 3.6, 3.7, and 3.8, just like before. The command to create a new environment is, conda create -n test -c cctbx-dev cctbx python=<python version> If "python=<python version>" is left out, the default Python version will be 3.8. To install cctbx into the currently active conda environment, the command is, conda install -c cctbx-dev cctbx The packages are currently on the cctbx-dev channel, but the goal is to get official packages into conda-forge. To get the cctbx recipe into conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021), we'll need an official release. I've opened up an issue on GitHub ( https://github.com/cctbx/cctbx_project/issues/451). Please provide any feedback on the versioning system, release schedule, and anything release related. Let us know if you're scripts are not working with these packages. 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

3 4

Python 2 only code
by Winter, Graeme (DLSLtd,RAL,LSCI) 04 Mar '20

04 Mar '20

Morning all, Looking at commits overnight saw https://github.com/cctbx/cctbx_project/commit/69d506ebd0ac212b8166eec98a8d8… which adds Python 2 only code to cctbx - I thought there were things in place which prevent regressions such as this? Error: the following jobs returned non-zero exit codes or suspicious stderr output: libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/iotbx/pdb/tst_hierarchy.py" [FAIL] 1.0s Time: 1.04 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/Users/graeme/svn/cctbx/modules/cctbx_project/iotbx/pdb/tst_hierarchy.py", line 7082, in <module> exercise(sys.argv[1:]) File "/Users/graeme/svn/cctbx/modules/cctbx_project/iotbx/pdb/tst_hierarchy.py", line 7069, in exercise exercise_other() File "/Users/graeme/svn/cctbx/modules/cctbx_project/iotbx/pdb/tst_hierarchy.py", line 5845, in exercise_other assert pdb_hierarchy.contains_protein() File "/Users/graeme/svn/cctbx/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1623, in contains_protein classes=['common_amino_acid', 'modified_amino_acid']) File "/Users/graeme/svn/cctbx/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 214, in get_n_residues_of_classes for resname, count in self.resnames.iteritems(): AttributeError: 'dict' object has no attribute ‘iteritems’ Given how much noise you will receive if you leave trailing whitespace in there, I’d like to think real errors like this would be picked up automatically? 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

1 0

IUCr2020 Computing School in Nove Hrady - 17th to 22nd August - Registration opened
by Claudia Millán Nebot 24 Feb '20

24 Feb '20

Dear all, We announce the IUCr Computing School in Nove Hrady (Czech Republic) which will take place between 17th and 22nd August 2020 prior to the IUCr Congress in Prague. Registration has already started. Further information about the school can be found on the website: https://www.xray.cz/iucr/workshops/nh/default.htm. Follow also our hashtag on Twitter, #IUCr2020CompSchool. Active developers of crystallographic software, tools and methods are invited to participate at this Computing School. The school is not introductory and it is recommended that participants already have some basic programming skills and crystallographic knowledge. Our aim is to discuss and exchange ideas and to tackle the challenges related to the method development in crystallography. Participants can be early-career scientists (PhD students, Postdocs, etc.) as well as established developers. Our confirmed speakers are: - Simon Billinge (Columbia University, USA) - Luc Bourhis (Bruker, France) - Paul Boyle (Western University, London, Ontario, Canada) - Iracema Caballero (Institut de Biologia Molecular de Barcelona, Spain) - Gemma de la Flor (Karlsruhe Institute of Technology, Germany) - Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) - Rafiga Masmaliyeva (Institute of Molecular Biology and Biotechnology, Azerbaijan) - Garib Murshudov (Laboratory of Molecular Biology-MRC, UK) - Reinhard Neder (Institute of Condensed Matter Physics, Erlangen, Germany) - Alexandre Ourjoumtsev (Institut de Génétique et de Biologie Moléculaire et Cellulaire, France) - Randy Read (University of Cambridge, UK) - Massimo Sammito (University of Cambridge, UK) - Arkadiy Simonov (Eidgenössische Technische Hochschule Zürich, Switzerland) - Melanie Vollmar (Diamond Light Source Ltd, Harwell Science & Innovation Campus, United Kingdom) - Thomas White (Center for Free-Electron Laser Science, Hamburg, Germany) For any questions regarding the school please contact us. Best wishes, Claudia Millán (cmncri at ibmb.csic.es) Martin Lutz (m.lutz at uu.nl) Jan Rohlicek (rohlicek at fzu.cz) PD. Please find attached a poster about the school that you can forward, together with this email, to people potentially interested in participating in the Computing School.

1 0

map grid sizes
by GEORGE N PHILLIPS 21 Feb '20

21 Feb '20

I am confused about grid sizes of maps. When i specify a grid size for an fft_map but then pull the numpy array out for direct manimpulation, it's always 2 larger in the last dimension. Why is it not the same size? Any help appreciated. George y# Now make initial (smoothed) map using random phases with Fobs f_obs_B = f_obs1.apply_debye_waller_factors( b_iso=biso_init) phases = f_obs_B.random_phases_compatible_with_phase_restrictions(deg=False) phases_data = phases.data() e_map_coeff = f_obs_B.phase_transfer(phase_source = phases_data) e_map = e_map_coeff.fft_map(crystal_gridding = crystal_gridding, symmetry_flags = maptbx.use_space_group_symmetry) print("cgridding", crystal_gridding.n_real()) # pick initial envelope e_map_array = e_map.real_map().as_numpy_array() print("e_map", e_map_array.shape) cgridding (90, 90, 80) e_map (90, 90, 82) George N. Phillips, Jr., Ph.D. Professor Emeritus University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone 713 348 6951 (Houston)

4 3

a little help for newbie?
by georgep 18 Feb '20

18 Feb '20

I am starting to write some python code using cctbx, but am missing how to use the C++ bindings. I am fine unless a try to access them. Something about my environment or boost of something. Can anyone point me in the right direction? I have import boost.python but am cleary missing some fundamental knowledge. George Traceback (most recent call last): File "/Users/georgep/PycharmProjects/test_env/HIO_Version3.py", line 225, in <module> S0 = percentile[rho_calc_true > percentile(rho_calc_true, solv_frac)] = 1 File "/Users/georgep/PycharmProjects/test_env/HIO_Version3.py", line 216, in percentile order = flex.sort_permutation(x) Boost.Python.ArgumentError: Python argument types in scitbx_array_family_flex_ext.sort_permutation(double) did not match C++ signature: sort_permutation(scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, bool reverse=False, bool stable=True) sort_permutation(scitbx::af::const_ref<unsigned long, scitbx::af::trivial_accessor> data, bool reverse=False, bool stable=True) sort_permutation(scitbx::af::const_ref<int, scitbx::af::trivial_accessor> data, bool reverse=False, bool stable=True) George N. Phillips, Jr. Ralph and Dorothy Looney Professor BioSciences at Rice Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 www.phillipslab.org

2 1

CCTBX documentation questionnaire
by Dorothee Liebschner 14 Jan '20

14 Jan '20

Hi everyone, During this year's ECM computing school, it came up that the CCTBX does not have a lot of documentation. This seems to be a major reason why people don't use it, even if they would like to employ the libraries. We would like to find out which parts of the CCTBX are the most interesting for users. We certainly cannot provide extensive documentation for the entire toolbox, but we can see what we can do once we know the main areas of interest. So if you were in the situation of wanting to use the CCTBX but decided to stay away from it because the documentation was non-existent or obscure, please let us know by filling out the questionnaire below (it's anonymous): questionnaire CCTBX documentation <https://forms.gle/9RawJFfHyEvhCVVP7> Best wishes, Dorothee -- Project 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

11 40