March 2020 - cctbxbb - phenix-online.org

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