- cctbxbb - phenix-online.org

mtz2map gridding
by Elliot Nelson 22 Feb '19

22 Feb '19

Hi All, I've been trying to use Phenix.mtz2map to sample maps to a particular array size with the "gridding" option, but found that this seems to have no effect on the output of the program. I was wondering whether there were some restrictions to the integers that are permitted or otherwise what might be the cause of this behaviour. Having hunted through the code it seems to just set n_real in the crystal gridding, which is then fed into an fft - possibly the latter ignores n_reals that aren't sensible? Any idea? Thanks, Conor on behalf of Conor Wild: conor.wild(a)oriel.ox.ac.uk Elliot DPhil Student, Systems Approaches to Biomedical Science<http://www.sabsidc.ox.ac.uk/> Protein Crystallography<http://www.thesgc.org/groupprofile/9489>, Structural Genomics Consortium, NDM, University of Oxford Oxford Protein Informatics Group<http://opig.stats.ox.ac.uk/>, Department of Statistics, University of Oxford

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OpenMP in fftpack
by Keitaro Yamashita 31 Jan '19

31 Jan '19

Dear CCTBX/PHENIX developers, According to PHENIX FAQ: https://www.phenix-online.org/documentation/faqs/index.html#general > In addition to these options, it is also possible to compile phenix.refine and Phaser with the OpenMP library, which automatically parallelizes specific instructions such as the FFT. This requires using the source installer for Phenix, and adding the argument "--openmp" to the install command. Because of threading conflicts, OpenMP is not compatible with the Phenix GUI. FFT in phenix.refine can be parallelized if OpenMP is enabled. However, it seems incorrect since 2017 due to this change: https://github.com/cctbx/cctbx_project/commit/3e932248e0491847a04ddeee429f8… The FAQ may need updating, but I am curious to know why it is disabled now. Best regards, Keitaro

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This is a test
by Billy Poon 29 Jan '19

29 Jan '19

The Phenix website was down for a few hours, so this is a test to see if the bulletin board is working. -- 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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Re: [cctbxbb] [git/cctbx] master: Fix typo geobox (1ad3fe055)
by Pavel Afonine 23 Dec '18

23 Dec '18

Bad idea to hard-wire package name into lowest level code. Now imagine we need the same for afit, amber, quantumbio, rosetta, etc.. Are we going to have a page-long block of "if" statements. Please re-think and remove. For example, whether you want to shift it or not can be a parameter that you cast way level up in the context specific code. Pavel On 12/20/18 09:53, CCTBX commit wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------------------------------------------------ > > > commit 1ad3fe05571162839e770c35ed032a7fc38a33b7 > Author: Gydo van Zundert <gydo.vanzundert(a)schrodinger.com> > Date: Wed Dec 19 14:58:36 2018 -0500 > > Fix typo geobox > > > ------------------------------------------------------------------------ > > > 1ad3fe05571162839e770c35ed032a7fc38a33b7 > mmtbx/refinement/real_space/individual_sites.py | 4 ++-- > 1 file changed, 2 insertions(+), 2 deletions(-) > > diff --git a/mmtbx/refinement/real_space/individual_sites.py > b/mmtbx/refinement/real_space/individual_sites.py > index c61e88b01..20f38a6b0 100644 > --- a/mmtbx/refinement/real_space/individual_sites.py > +++ b/mmtbx/refinement/real_space/individual_sites.py > @@ -350,7 +350,7 @@ class box_refinement_manager(object): > > # When using the Schrodinger force field, move the whole > structure as the > # selected atoms are environment aware. > - if geobox.get_source() == 'SCHRODINGER': > + if geo_box.get_source() == 'SCHRODINGER': > geo_box.shift_cart(box.shift_cart) > > rsr_simple_refiner = simple( > @@ -377,7 +377,7 @@ class box_refinement_manager(object): > iselection, sites_cart_refined) > self.xray_structure.set_sites_cart(sites_cart_moving) > self.sites_cart = self.xray_structure.sites_cart() > - if geobox.get_source() == 'SCHRODINGER': > + if geo_box.get_source() == 'SCHRODINGER': > geo_box.shift_cart(shift_back) > else: # NCS constraints are present > # select on xrs, grm, ncs_groups > > ------------------------------------------------------------------------ > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 >

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Broken iotbx/pdb/cif test
by richard.gildea＠diamond.ac.uk 20 Dec '18

20 Dec '18

According to Jenkins these two tests have been broken for several days - does anyone know what the issue is and could a fix be applied? Both look like the same error. iotbx/regression/tst_pdb_as_cif.py iotbx/regression/tst_data_manager.py These have been failing since this commit: https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c… The tests also fail locally for me (not just on Jenkins). Cheers, Richard Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module> exercise_01() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01 logger=null_out(), File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program task.run() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run txt = model.model_as_mmcif() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif if self.get_restraints_manager() is not None: File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager self.setup_restraints_manager() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager self._process_input_model() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom entry = cif_types.energy_lib_atom(**dict(row)) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__ raise_value_error("Floating-point") File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7 Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 532, in <module> test_model_datatype() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 233, in test_model_datatype dm.get_model().model_as_mmcif(), overwrite=True) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif if self.get_restraints_manager() is not None: File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager self.setup_restraints_manager() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager self._process_input_model() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom entry = cif_types.energy_lib_atom(**dict(row)) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__ raise_value_error("Floating-point") File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7 Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- 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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forcing building boost_python early in SConscript
by Robert Oeffner 18 Nov '18

18 Nov '18

We are working on a newer version of Phaser. The new SConscript file for Phaser imports features from boost_python. Therefore it is currently not straightforward to build it since an empty build directory does not yet contain the boost_python module to be imported by SConscript (or python). So SCons crashes when it reads the new Phaser SCsonscript stating that boost_python cannot be imported. Currently our workaround is to first build CCTBX alone and then subsequently to build Phaser. My question is if it is possible to specify dependencies in cctbx_project/boost_adaptbx/SConscript to force building boost_python early on. On Windows boost_thread and a few other libraries are built before other SConscript files are read. So I have put some Depends(boost_thread, boost_python) andDepends(boost_thread, boost_python_meta_ext) statements into cctbx_project/boost_adaptbx/SConscript. These do seem to force building the boost_python.lib and .dll files. But building the boost_python_meta_ext python module fails with the error: boost_adaptbx\meta_ext.cpp(14): fatal error C1083: Cannot open include file: 'boost_adaptbx/type_id_eq.h' It's possible that I'm not using SCons as it's supposed to be used. Let me know if anyone has a suggestion on how to force building boost_python before other SConscript are read. 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 Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

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Fwd: Re: indexing diffraction pattern
by Pavel Afonine 15 Nov '18

15 Nov '18

Perhaps someone can reply Wen.. Pavel -------- Forwarded Message -------- Subject: Re: indexing diffraction pattern Date: Sat, 10 Nov 2018 09:30:53 -0500 From: Wen Jiang <jiang12(a)purdue.edu> To: Pavel Afonine <pafonine(a)lbl.gov> Pavel, Sorry for insufficient details. The scenario is that I have a numpy 2D array of float values that represents an image of "diffraction pattern" (generated by an image processing operation, not actual X-ray diffraction). I need to determine the peak positions and then find a 2D lattice (two 2D vectors) going through these peaks. I have my own simple functions that can detect the peaks and find a 2-D lattice to cross the peaks but it often fails when the "diffraction pattern" is not very clean. Thus, I want to find a more robust method that works well when the peaks are relatively weak, not very sharp, and when there are some spurious peaks off the lattice. I think these tasks are exactly what cctbx has solved for indexing X-ray diffraction images. Hope that these explanations help clarify the problem. Thanks, Wen Prof. Wen Jiang Department of Biological Sciences Department of Chemistry (Courtesy) Scientific Director, Purdue Cryo-EM Facility Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 http://jiang.bio.purdue.edu On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine(a)lbl.gov <mailto:[email protected]>> wrote: Hi Wen, I'm not sure I fully understand your question... You say a function that takes a numpy array.. Array of what? Then, "a list of diffraction spots" -- these are measured in diffraction experiment. If you could provide more details as to what you are trying to do as well as what exactly the inputs are then I will do my best to see how to do this in CCTBX or forward your questions to CCTBX mailing list so that others can comment. All the best, Pavel On 11/10/18 03:56, Wen Jiang wrote: > Hi Pavel, > I am looking for a function that takes a numpy array and returns a > list of diffraction spots and lattice vectors. I think > cctbx should have such a function but I am not familiar with it. > Can you point me in the right direction? > Thanks, > > Wen > > Prof. Wen Jiang > Department of Biological Sciences > Department of Chemistry (Courtesy) > Scientific Director, Purdue Cryo-EM Facility > Purdue University > Hockmeyer Hall of Structural Biology > 240 S. Martin Jischke Drive > West Lafayette, IN 47907 > http://jiang.bio.purdue.edu >

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Windows woes
by Luc Bourhis 10 Nov '18

10 Nov '18

Hi, Trying to install cctbx on Windows 10, 1. install latest python 2 from Python.org 2. python2 bootstrap.py —builder=cctbxlite —with-python=\path-to-python-from-step-1 It fails because of missing module “builtins”. So I installed pip, then used it to install “future”. Then I had to install “six” with pip. Am I being stupid or cctbx does not install out of the box anymore? Best wishes, Luc J Bourhis

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Python 3 and CCP4
by David Waterman 02 Nov '18

02 Nov '18

Hi folks, It's great to see the momentum building behind the project to migrate to Python 3. From the roadmap <https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap>, there is clearly still some way to go, but current activity makes me wonder if the proposed deadline of complete migration by 2020 might be beaten easily. What is not clear from the roadmap is whether there are any plans for a post-transition grace period, in which we have switched from writing forwards compatible Python 2 code to writing backwards compatible Python 3 code. Has this been thought about? Or will it be the case that the first commit of Py3-only code seals the deal? I ask because CCP4 has to support a large number of Python projects and these have not all considered the Python 3 switch nearly as seriously as cctbx yet. What I would like to request is a reasonable period of backwards compatibility is ensured to allow other CCP4 projects to catch up, and that this protected period is enshrined within the roadmap or developer guidelines. What do you think? Best wishes -- David

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construct hkl arrays from number of reflections and resolution
by Robert Oeffner 29 Oct '18

29 Oct '18

I would like a function that spits out an HKL array as a function of number of reflections, dmin and dmax. It's quite likely this has already been done somewhere in the CCTBX. Would anyone know if this is the case rather than me having to reinvent the wheel? 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 Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

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