- cctbxbb - phenix-online.org

Experimental gradients
by Kristoffer Lundgren 10 Oct '23

10 Oct '23

Hello all, I am wondering if it is possible to use cctbx to calculate gradients from experimental data? Both in reciprocal and real space is of interest. Are there any code examples available somewhere showcasing how this can be achieved? Best regards Kristoffer Lundgren

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iterating over crystals
by David Waterman 17 Sep '23

17 Sep '23

Hi folks, I'm testing some code changes and would like to iterate over every space group and for each generate a random unit cell compatible with the Bravais symmetry. I've got the iteration sorted with space_group_symbol_iterator, but I'm not sure how best to generate some compatible unit cell from the space_group object. Is this something I could do easily with cctbx? Cheers, -- David

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Unexpected (to me) behavior of flex.bool
by Pavel Afonine 17 Jun '23

17 Jun '23

Hi All, today it took me several hours to debug something that ended up being the result of this behavior: >>> from scitbx.array_family import flex >>> x = flex.bool(True, 5) >>> y = flex.bool(5, True) >>> list(x) [True] >>> list(y) [True, True, True, True, True] >>> I needed to pass a flex.bool array (with all True) into a C++ function and I was doing it as "x" above. In that C++ function there was no size check for incoming arrays (bad idea!) and then later in the code when accessing elements of this flex.bool array I was getting "random" numbers! I was pretty sure that flex.bool(True, 5) should lead to an assertion error! Was this always like this (and I was just super-lucky to never run into this issue in the past 20 years) or something has changed? Pavel

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any plans for PDB files with long CCD codes?
by Marcin Wojdyr 16 May '23

16 May '23

Hello Cctbx and Phenix developers, as you know, extended CCD codes arrive this year. I'm looking into examples https://github.com/wwPDB/extended-wwPDB-identifier-examples and thinking what's the best way to convert such files to PDB. Do you plan anything in this matter, like it was done with https://cci.lbl.gov/hybrid_36/ in the past? Tentatively, I'm thinking about mapping residue names in the HETNAM record. For example, BB87Q would be mapped to a "3 letter code" that code would have a special character to make it different from normal 3-letter codes (let's say '%', or maybe '+' or '_' - I don't have a strong preference), and the original CCD code would be given in columns 72-79 of HETNAM that are currently unused: HETNAM BB% PHOSPHOSERINE [...] BB87Q

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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

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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

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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

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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

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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

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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…>

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