- cctbxbb - phenix-online.org

pull request - fable
by Nic Gould 15 May '23

15 May '23

Hi All, Sorry for the intrusion, the Github page suggests contacting the devs on the mailing list before making a pull request. I ran into some minor issues building fable and was wondering if it's worth submitting a pull request. - invalid pre-processor directive (fixed upstream at boost https://github.com/boostorg/thread/issues/364) - Invalid python API call ( fixed upstream at boost here https://github.com/boostorg/python/pull/344) - Need to install python.h : This one seems tricky as it varies between platforms and it's probably not a 'you problem'. Maybe add a line to the setup documentation. Interestingly it needs to be installed on the host machine, not in the conda venv. Kind regards Nic Gould

2 1

Potential website disruptions
by Billy Poon 11 Apr '23

11 Apr '23

Hi everyone, We are doing some maintenance on our websites, https://phenix-online.org and https://cci.lbl.gov, over the next few days. There may be some disruptions. Thanks in advance for your patience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

1 0

github host key
by Robert Oeffner 24 Mar '23

24 Mar '23

Am I the only one being unable to push or pull from the CCTBX repo and instead getting a warning that the host github key has changed or that somebody is eavesdropping on me? Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus The Keith Peters Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

3 3

Python 3.11
by Luc Bourhis 15 Dec '22

15 Dec '22

Hi,may I enquire about the time table for Python 3.11 compatibility? We are planning to move to it as soon as possible at Bruker, hence my question.Best wishes,Luc Bourhis

3 8

Conda dropping Python 3.7 real soon now
by Winter, Graeme (DLSLtd,RAL,LSCI) 16 Sep '22

16 Sep '22

Hi All, Possibly of relevance herein - https://conda-forge.org/docs/user/announcements.html#dropping-python-3-7 "Conda-Forge has been providing support for Python 3.7 for 4 years now. Increasingly projects are moving off it (particularly in the PyData community). With Python 3.11’s release coming around the corner (October 3rd), conda-forge plans to drop Python 3.7 support when Python 3.11 comes out. This will lighten the load on conda-forge infrastructure and make room for the new versions the community would like to support.” ISTR PHENIX is pinned on 3.7 right now because of some non-3.8 compatible code? That could become more of a problem Cheerio 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

Next conda version?
by Luc Bourhis 13 Sep '22

13 Sep '22

Hi, I have just fixed a bug introduced a few years ago that broke some of our code at Bruker. We use conda to add the cctbx to our environment, hence my question: when can the next version be expected on conda-force including that fix? No pressure! I would like to know to plan ahead. Thanks! Best wishes, Luc https://github.com/cctbx/cctbx_project/commit/085f6d8cf57b91dce3a695ebbfbcf… <https://github.com/cctbx/cctbx_project/commit/085f6d8cf57b91dce3a695ebbfbcf…>

4 4

boost python exports
by David Waterman 02 Mar '22

02 Mar '22

Hi folks, I'm trying to create a boost python class that works with either vec3 or mat3 arrays (and I only need those two types). I made a templated class and then exported it twice with different names, for the vec3 and mat3 versions. For example, for mat3: class_<ReconstituteDerivatives< mat3<double> > >("ReconstituteDerivativesMat3", no_init) .def("get_data", &ReconstituteDerivatives< mat3<double> >::get_data) .def("get_indices", &ReconstituteDerivatives< std::size_t >::get_indices); I can create one of these objects from Python >>> foo <dials_refinement_helpers_ext.ReconstituteDerivativesMat3 object at 0x7f3ffa421ac0> but the accessors are not exported properly: >>> foo.get_data() Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: No to_python (by-value) converter found for C++ type: scitbx::af::shared<scitbx::mat3<double> > I expected a scitbx_array_family_flex_ext.mat3_double here >>> foo.get_indices() Traceback (most recent call last): File "<stdin>", line 1, in <module> Boost.Python.ArgumentError: Python argument types in ReconstituteDerivativesMat3.get_indices(ReconstituteDerivativesMat3) did not match C++ signature: get_indices(dials::refinement::ReconstituteDerivatives<unsigned long> {lvalue}) and I expected a scitbx_array_family_flex_ext.size_t here. Is it likely there is something simple I am missing, like a #include? I do include flex_wrapper.h. Or perhaps I am just doing something wrong with templated classes and boost python. Looking at other code isn't helping to reveal the mysteries to me yet. Cheers -- David

1 2

DYLD_FALLBACK_LIBRARY_PATH
by Winter, Graeme (DLSLtd,RAL,LSCI) 04 Jan '22

04 Jan '22

Hi Folks, By default cctbx dispatchers on macOS clobber DYLD_FALLBACK_LIBRARY_PATH with some stuff which means that from napari import viewer fails with a huge stack trace ending in OSError: dlopen(libobjc.dylib, 6): image not found If I comment out the clobbering in the dispatcher then everything works fine so I am fairly sure this is the problem Some questions - - why do we do this? - is there a way I can make a dispatcher not to this? or maybe leave the system DYLD… as it was and _append_ to rather than prepend? Seems like a thing I am surprised I have not broken a toe on before now Thanks 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

2 8

Re: [cctbxbb] [git/cctbx_project] master: Reduce2: place NH3 only at residue with resseq 1. (765881e87b)
by Pavel Afonine 10 Nov '21

10 Nov '21

What if chain starts with a number different than 1 (people tend to number chain residues in many different ways, even using negative numbers, and they claim they have valid reasons to do so)? iotbx.pdb.hierarchy has a clear definition of the chain. So I'd suggest adding NH3 to the fist residue of the chain, no matter what that residue number is. Pavel On 11/10/21 14:03, CCTBX commit wrote: > Repository : https://github.com/cctbx/cctbx_project/ > On branch : master > Link : > https://github.com/cctbx/cctbx_project/commit/765881e87b5982c3b68e8dcd8c0e0… > > ------------------------------------------------------------------------ > > > commit 765881e87b5982c3b68e8dcd8c0e00c61c5b5600 > Author: dcliebschner <dcliebschner(a)lbl.gov> > Date: Wed Nov 10 14:03:06 2021 -0800 > > Reduce2: place NH3 only at residue with resseq 1. > > > ------------------------------------------------------------------------ > > > 765881e87b5982c3b68e8dcd8c0e00c61c5b5600 > mmtbx/hydrogens/reduce_hydrogen.py | 19 +- > mmtbx/hydrogens/tst_add_hydrogen.py | 196 ++++++++--------- > mmtbx/hydrogens/tst_add_hydrogen_2.py | 383 > ++++++++++++++++------------------ > 3 files changed, 282 insertions(+), 316 deletions(-) > > Diff suppressed because of size. To see it, use: > > git diff-tree --root --patch-with-stat --no-color > --ignore-space-at-eol --textconv --ext-diff --cc > 765881e87b5982c3b68e8dcd8c0e00c61c5b5600 > ------------------------------------------------------------------------ > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCTBX-COMMIT&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCTBX-COMMIT&A=1> >

1 0

accessing attributes of PHIL parameters
by Robert Oeffner 15 Oct '21

15 Oct '21

Hi, Most likely a trivial question but if I have a PHIL object such as one based on the string arrayinfo_phil_str = """ selected_info { span = True .type = bool .short_caption = "Span" minmax_data = True .type = bool .short_caption = "min,max data" } """ I can then get the PHIL definitions span and minmax_data as python values like: from libtbx.phil import parse parse(arrayinfo_phil_str).extract().selected_info.span parse(arrayinfo_phil_str).extract().selected_info.minmax_data But how do I access the values of the short_caption attribute of these definitions? Does that make sense or have not understood correctly how PHIL works? Thanks, Rob -- This email has been checked for viruses by AVG. https://www.avg.com

2 1