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

Timestamp:

Apr 8, 2024, 4:18:11 PM (19 months ago)

Author:

Tom Goddard

Comment:

--

Dev2024-4-8

@@ -20 +20 @@
 = Discussion =
 
+* How to handle MTZ format when Toolshed cache not initialized
+  - 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.
+  - Discussed 8 possible solutions.
+  - Currently Eric downgraded error to an info message.
+  - Eric will reevaluate which solution is best.
+
+* PyTables failing to read some HDF5 files
+  - New pytables in daily build fails to read some EMAN HDF5 files that ChimeraX 1.7 read.
+  - Tom will probably revert PyTables version.
+
+* Cython on Mac ARM
+  - Tristan had a problem where Cython not in Mac ARM builds.
+  - Greg believes it is fixed, by compiling Mac ARM Cython separately, and will ask Tristan.
+
+* Medical imaging on Toolshed
+  - Zach working on putting medical imaging in Toolshed.
+  - Enhancing Toolbar interface to be able to remove buttons and add buttons.
+  - Will add a button to medical imaging toolbar to install from toolshed.
+  - Will reconfigure Toolbars hiding molecule ones if user wants medical imaging user interface.
+
+* Sequence alignments from structure alignments
+  - Eric porting Chimera ability to make sequence alignments from structure alignments.
+  - Case of two structures is easy, but more than two is very hard.
+  - Working on more than 2 in C++ where it was in Python (and very slow) in Chimera.
+
+* Klim Verba meeting tomorrow, comparing kinases
+  - Tom is meeting Klim Verba and grad student tomorrow to discuss how to compare tens to hundreds of kinases.
+  - Interested in seeing sequence differences and conformation differences.
+  - Interested in how to locate related structures, maybe BLAST of PDB.
+  - Klim's group analyzes kinase sustrate specificity.
+
+* python_instances_of_class crash
+  - Eric has fixed an often reported crash in daily build where C++ mapping from C++ object (e.g. Atom) to Python object became invalid.
+  - Sequence __del__ method was not called and so pointer to freed Python objects in C++ table were not being removed.
+
+* Replace PyQt with PySide6?
+  - PyQt license needs to be renewed this month.
+  - Might want to try replacing PyQt with PySide6 after ChimeraX 1.8 is released.
 
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