Changes between Version 1 and Version 2 of Dev2024-4-8


Ignore:
Timestamp:
Apr 8, 2024, 4:18:11 PM (20 months ago)
Author:
Tom Goddard
Comment:

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  • Dev2024-4-8

    v1 v2  
    2020= Discussion =
    2121
     22* How to handle MTZ format when Toolshed cache not initialized
     23  - Looked at ticket #14862 startup error caused by PDB-Redo registering MTZ fetch when Toolshed not initialized so it didn't know Clipper on Toolshed provides MTZ reading.
     24  - Discussed 8 possible solutions.
     25  - Currently Eric downgraded error to an info message.
     26  - Eric will reevaluate which solution is best.
     27
     28* PyTables failing to read some HDF5 files
     29  - New pytables in daily build fails to read some EMAN HDF5 files that ChimeraX 1.7 read.
     30  - Tom will probably revert PyTables version.
     31
     32* Cython on Mac ARM
     33  - Tristan had a problem where Cython not in Mac ARM builds.
     34  - Greg believes it is fixed, by compiling Mac ARM Cython separately, and will ask Tristan.
     35
     36* Medical imaging on Toolshed
     37  - Zach working on putting medical imaging in Toolshed.
     38  - Enhancing Toolbar interface to be able to remove buttons and add buttons.
     39  - Will add a button to medical imaging toolbar to install from toolshed.
     40  - Will reconfigure Toolbars hiding molecule ones if user wants medical imaging user interface.
     41
     42* Sequence alignments from structure alignments
     43  - Eric porting Chimera ability to make sequence alignments from structure alignments.
     44  - Case of two structures is easy, but more than two is very hard.
     45  - Working on more than 2 in C++ where it was in Python (and very slow) in Chimera.
     46
     47* Klim Verba meeting tomorrow, comparing kinases
     48  - Tom is meeting Klim Verba and grad student tomorrow to discuss how to compare tens to hundreds of kinases.
     49  - Interested in seeing sequence differences and conformation differences.
     50  - Interested in how to locate related structures, maybe BLAST of PDB.
     51  - Klim's group analyzes kinase sustrate specificity.
     52
     53* python_instances_of_class crash
     54  - Eric has fixed an often reported crash in daily build where C++ mapping from C++ object (e.g. Atom) to Python object became invalid.
     55  - Sequence __del__ method was not called and so pointer to freed Python objects in C++ table were not being removed.
     56
     57* Replace PyQt with PySide6?
     58  - PyQt license needs to be renewed this month.
     59  - Might want to try replacing PyQt with PySide6 after ChimeraX 1.8 is released.
    2260
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