- cctbxbb - phenix-online.org

Adding more parameters to xray::scatterer for anharmonic thermal displacements
by Luc J. Bourhis 22 Aug '18

22 Aug '18

Hi, we are working with Michal Chodkiewicz (Warsaw University) to add anharmonic thermal tensors to smtbx refinement. I was thinking to add one pointer to xray::scatterer, which can be NULL. When it is not so, it would point to an object which can compute the value and the derivatives for that thermal factor. That means we would have a base class with virtual methods, but I would say that is our problem! The issue for the rest of the cctbx community is the extra storage of that pointer in that class. Would that be all right? I remember quite a few years ago Ralf saying he wanted to replace the ADP's by a pointer to an external storage to save space. Our idea is along the same line. Best wishes, Luc

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model selection
by Pavel Afonine 16 Aug '18

16 Aug '18

Currently model class has three selection methods: def selection(self, selstr, optional=True): def select(self, selection): def iselection(self, selstr): which is hideously confusing with zero chance to remember, and also inconsistent with the rest. Most objects in cctbx have ".select(self, selection)" methods, while being inconsistent about what they expect: iselection or boolean selection as "selection" argument. Some smart ones though can take both int or bool selections (figure out type automatically, which is trivial). Can we consolidate all three into one ".select()" that would allow taking bool or int or str? Or you think there are philosophical arguments against it? Pavel On 8/16/18 15:00, CCTBX commit wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------------------------------------------------ > > > commit c98b44997e8eb7bf53ee828f510b933cd5167758 > Author: Oleg Sobolev <osobolev(a)lbl.gov> > Date: Thu Aug 16 15:00:20 2018 -0700 > > Proper use of model class > > > ------------------------------------------------------------------------ > > > c98b44997e8eb7bf53ee828f510b933cd5167758 > mmtbx/model/model.py | 3 +-- > 1 file changed, 1 insertion(+), 2 deletions(-) > > diff --git a/mmtbx/model/model.py b/mmtbx/model/model.py > index 6f2247452..87412f95c 100644 > --- a/mmtbx/model/model.py > +++ b/mmtbx/model/model.py > @@ -2312,8 +2312,7 @@ class manager(object): > sizes = flex.int() > h = self.get_hierarchy() > if(macro_molecule_only): > - asc = h.atom_selection_cache() > - s = asc.selection("protein or nucleotide") > + s = self.selection("protein or nucleotide") > h = h.select(s) > for r in h.residue_groups(): > sizes.append(r.atoms().size())

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Extracting data from MTZ
by David Waterman 14 Aug '18

14 Aug '18

Hi all, I have a script that extracts Fobs and Fcalc from an MTZ file produced by Refmac for some analysis. I was just doing this in a trivial way: fobs = m.extract_reals("F").data fc = m.extract_reals("FC_ALL").data and this worked fine, until I came across a file with missing observations, so that the lengths of fobs and fc do not match. Can anybody advise a better way to do this please? I'm inexperienced with iotbx.mtz. I don't need anything other than the values of the structure factors, but I need each element of fobs and fc to contain the equivalent values. Thanks -- David

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How does Jenkins work?
by Takanori Nakane 28 Jul '18

28 Jul '18

Hi, Why does Jenkins still run tests on my old commits on my deleted (dxtbx-sacla) branch? The test failure is probably caused by my commit dc17165 but I committed a fix 5c7416b and confirmed that it passes the tests. So I merged my topic branch to master and deleted the branch from GitHub. I know how git works but I am new to the practice in the cctbx repository (like using rebase instead of merge). If I am doing something wrong, could you please point it to me? Best regards, Takanori Nakane > <html><head></head><body><table style="width:100%; background-color: > #F59400; color: #FFF; border-radius: 0.5em; margin-bottom: 0.5em"><tr><td > style="margin: 0.5em 1.25em 0.5em 0.7em; font-weight: bold; font-family: > sans-serif; font-size: 110%"><a > href="http://jenkins.diamond.ac.uk:8080/job/cctbx_branch_tests/145/" > style="color:#FFF; text-decoration: none"><big>Build CCTBX Branch Tests is > unstable</big></a></td></tr></table><br/><table style="width:100%; > background-color: #F59400; color: #FFF; border-radius: 0.5em; > margin-bottom: 0.5em"><tr><td style="margin: 0.5em 1.25em 0.5em 0.7em; > font-weight: bold; font-family: sans-serif; font-size: 110%"><a > href="http://jenkins.diamond.ac.uk:8080/job/cctbx_branch_tests/145/testReport" > style="color:#FFF; text-decoration: none">3 out of 940 tests failed (132 > skipped)</a></td></tr></table><table style="margin: 0.5em 0 1em > 2em"><tr><td><pre style="font-size:80%">3 tests failed. > FAILED: > dxtbx.build_dials.modules.cctbx_project.dxtbx.tests.test_regression_images.test_no_multiple_format_understanding[SACLA_MPCCD_Cheetah/run266702-0-subset.h5] > Error Message: > exit code 1 > Stack Trace: > FAILED: > dxtbx.build_dials.modules.cctbx_project.dxtbx.tests.test_regression_images.test_no_multiple_format_understanding[putative_imgCIF_HDF5_mapping/minicbf.h5] > Error Message: > exit code 1 > Stack Trace: > FAILED: > dxtbx.build_dials.modules.cctbx_project.dxtbx.tests.test_regression_images.test_no_multiple_format_understanding[putative_imgCIF_HDF5_mapping/X4_wide_M1S4_1.nxs] > Error Message: > exit code 1 > Stack Trace: > </pre></td></tr></table><table style="width:100%; background-color: > #F59400; color: #FFF; border-radius: 0.5em; margin-bottom: 0.5em"><tr><td > style="margin: 0.5em 1.25em 0.5em 0.7em; font-weight: bold; font-family: > sans-serif; font-size: 110%">Changes since the last successful > build</td></tr></table><table style="margin: 0.5em 0 1em > 2em"><tr><td><table style="padding: 0.1em 0.4em; background-color: > #F59400; color:#fff"><tr><td>145</td></tr></table></td><td>No changes > </td></tr></table><table style="width:100%; background-color: #CCC; color: > #000; border-radius: 0.5em; margin-bottom: 0.5em"><tr><td style="margin: > 0.5em 1.25em 0.5em 0.7em; font-weight: bold; font-family: sans-serif; > font-size: 110%">Build environment</td></tr></table><table style="margin: > 0.5em 0 1em 2em"><tr><td><span > style="font-size:130%"> [ </span>cctbx <strong>71a4ab94a > 2018-07-25 06:47:08 +0900</strong><span > style="font-size:130%"> | </span>DIALS regression > <strong>1924</strong>, PHENIX regression <strong>4419</strong>, DLS > Jenkins scripts <strong>8de8b58 2018-07-04 23:29:22 +0100</strong><span > style="font-size:130%"> ] </span></td></tr></table><span > style="color:#CCC;font-size:80%">mail template revision > 2487</span></body></html> > <br> > <hr> > <p align="center">To unsubscribe from the CCTBX-COMMIT list, click the > following link:<br> > <a > href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1" > target="_blank">https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1</a> > </p>

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mmtbx wilson_scaling in a small molecule context
by ben.williams＠diamond.ac.uk 23 Jul '18

23 Jul '18

Hello any and all, I was looking to make use of the functionality of wilson_scaling (Wilson plot, etc.) from mmtbx.scaling.data_statistics, in the context of small molecule data. I'm new to mmtbx, so here are two (groups of) questions for the enlightened: 1. Designed, as it is, with MX in mind, wilson_scaling's __init__ demands as an argument the number of protein residues, in order to form an estimate of the contents of the asymmetric unit. If this class were to be used in a small molecule context, what would be a sensible value to use? Would spoofing n_residues with an arbitrary small number (1?) be a robust bodge? Is it ever likely to howl? 2. Being crystals of small molecules, the samples in question may have inversion centres, mirror planes. Having been designed as a tool for MX, will wilson_scaling throw a wobbly when it sees my data? Many thanks, Ben Williams Diamond Light Source -- 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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subset of reflections from mtz object
by Robert Oeffner 18 Jul '18

18 Jul '18

Hi, I'm not as well versed using iotbx.mtz as I ought to be. I'd like to make a subset of reflections from an mtz file bounded by a chosen dmin and dmax, i.e. a resolution shell of reflections. What is the best way of doing this in python? 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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Citation for CCTBX
by Thomas, Jens 17 Jul '18

17 Jul '18

Hi, I'm updating the references printed by AMPLE and would like to cite CCTBX. Is there a recommended citation or way to acknowledge the use of CCTBX in a program? Best wishes, Jens

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cctbx debug build windows
by Pascal 10 Jul '18

10 Jul '18

Hi, How do you build a debug version of cctbx on windows? After getting an environement working with bootstrap, I reconfigured with configure.py --build=debug and it is now failing when linking against python27_d.lib Any advice? Pascal

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Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi everyone, The upcoming Phenix 1.14 official release will still have installers for CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life Cycle Support Add-On (until November 30, 2020), we are planning on deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are planning on deprecating 32-bit support for Windows because only a few percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are for 32-bit versions. Please let us know if support for CentOS 5 (32-bit and/or 64-bit) or 32-bit Windows is a requirement for your systems. If so, also please describe your setup. 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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Install OpenBLAS or MKL in base
by Luc Bourhis 22 Jun '18

22 Jun '18

Hi, years ago, I had wrote on this discussion list about a project of mine to dramatically accelerate scitbx.lstbx by using optimised BLAS libraries. That work had been dormant on a branch but now we are planning to move forward with the help of Pascal Parlois who will do the actual coding in the coming months. In order for this new code to be exercised by nightly tests, we, the smtbx people, need to write code so that that optimised BLAS library is installed during bootstrap. Right now, as a stopgap, I used conda to install either OpenBLAS and MKL but that won’t do with the cctbx philosophy. There are basically two choices: either OpenBLAS or MKL. When I started this project, I chose OpenBLAS because MKL was not freely redistributable, and I had got the green light to install it as needed. However now MKL has become completely free, thus becoming a possible choice. MKL is more performant on Intel but OpenBLAS is better on AMD (OpenBLAS actually runs on pretty much any processor out there but we don’t care in the context of cctbx): c.f. Julia people conclusions <https://discourse.julialang.org/t/openblas-is-faster-than-intel-mkl-on-amd-…> Now I realise that most of you may not care one way or another!?! But we won’t move forward before we got the green light… Note that I am taking about installing a BLAS usable from C++ here, not getting a BLAS-accelerated numpy. The latter could be an alternative though. But that would require to modify the bootstrap code to compile a MKL- or OpenBLAS-enabled numpy anyway. Best wishes, Luc J Bourhis

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