- cctbxbb - phenix-online.org

Windows 10 Retirement Date
by Billy Poon 27 May '25

27 May '25

Hi everyone, Microsoft will be dropping support for Windows 10 later this year on October 14, 2025. https://learn.microsoft.com/en-us/lifecycle/products/windows-10-home-and-pro Phenix intends to drop Windows 10 support after that date. Are there users where Windows 10 support is required after that date? Thanks! -- 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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reduce2 and cell construction from python script
by Enrico Ravera 14 Feb '25

14 Feb '25

Hi, I apologize for the naive post. I am trying to figure out how to perform the following tasks: 1) read in a mmcif file (which I think I can do following the tutorial); 2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial); 3) run reduce2 to get hydrogens in the nuclear positions (no clue); 4) get the full content of the unit cell (no clue). Any help is appreciated. All the best, Enrico

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getting indices of selected grid elements of a map
by robert＠oeffner.net 20 Jan '25

20 Jan '25

Hi, I am wondering if there is an efficient way to retrieve the 3D indices of a selection from a map. In the example on https://cci.lbl.gov/docs/cctbx/doc_low_flex_advanced/#getting-indices-of-se… it is shown how to list the indices of a subset of grid elements of the map as in print(list(isel)) But isel is a 1D representation of 3d map indices. What if I want to get hold of the list of 3D indices corresponding to the indices in the isel array? Is there a fast boost-python way of doing this or would I have to do a 3D loop over the unit cell grid numbers to see if enumerated grid elements matches any of the elements in the isel array? Many thanks, Rob

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atomic density profile at finite resolution
by robert＠oeffner.net 12 Dec '24

12 Dec '24

I came across this article https://doi.org/10.1107/S160057672201144X. Although I have yet to read it in details I wonder if the CCTBX can Fcalc maps at finite resolution, i.e. not using Gaussian atomic density profiles. It looks like the function in cctbx.maptbx.atom_curves.bcr_approx(...) is suited to do so. If so, how would I use this for generating a real space map as in https://cci.lbl.gov/docs/cctbx/script_1/#create-a-map-from-a-pdb-file but now using atomic density profiles at finite resolution? Many thanks, Robert

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cluster coordinates to asymmetric unit
by robert＠oeffner.net 05 Dec '24

05 Dec '24

Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this? Many thanks, Robert

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chiral validation
by James Holton 04 Nov '24

04 Nov '24

Can anyone tell me the units of the numbers being displayed by phenix.chiral_validation? The --help documentation doesn't mention anything about chirality. Seems to be a copy of the documentation for omegalyze? Just thought that might be of interest, and I also want to know what the numbers mean. Cheers, -James

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electron density value near an atom
by robert＠oeffner.net 14 Oct '24

14 Oct '24

Dear CCTBX users/developers I would like to calculate the theoretical electron density value at a point in space as a function of an atom specified by its coordinate and its form factor. I’ll assume it’s for a certain X-ray wavelength, say 1.0Å. If someone would have the time to give me a few pointers on how to do this using the CCTBX I'd be very grateful. Thanks in advance, Rob

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Hardware migration
by Billy Poon 19 Jun '24

19 Jun '24

Hi everyone, We are in the process of migrating these bulletin boards to new hardware over the next few weeks. I will make another post once the migration is completed. Nothing will be changed until then. Thanks! -- 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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Test thread from website
by bkpoon＠lbl.gov 19 Jun '24

19 Jun '24

The bulletin board update has also enabled posting from the website

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test post
by bkpoon＠lbl.gov 16 Jun '24

16 Jun '24

This is a test message

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test post
by bkpoon＠lbl.gov 16 Jun '24

16 Jun '24

This is a test message

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test post
by bkpoon＠lbl.gov 16 Jun '24

16 Jun '24

This is a test message

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Python 3.12 release schedule
by Luc Bourhis 15 Mar '24

15 Mar '24

Hi, I see in the commit that you guys are working on supporting Python 3.12. With the latest version of Python 3.11 on Anaconda, we have a compatibility issue between Qt that we use and ICU 70.1 that cctbx requires. The problem is solved by moving to Python 3.12, hence my question: when can we hope to see a release with Python 3.12? No pressure! Just trying to plan ahead. Best wishes, Luc

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Experimental gradients
by Kristoffer Lundgren 11 Oct '23

11 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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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

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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

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