- cctbxbb - phenix-online.org

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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