- cctbxbb - phenix-online.org

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 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

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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

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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

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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

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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

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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

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