id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
8975	Fix AlphaFold energy minimization	Tom Goddard	Tom Goddard	"Google Colab updated from Python 3.9 to 3.10 on April 28, 2023 (without announcing, grr) which broke ColabFold which required an old tensorflow version not available with Python 3.10.  ColabFold fixed that problem and I updated ChimeraX to use the new ColabFold.  Also OpenMM 7.5.1 install did not work with Python 3.10 so ColabFold updated it to OpenMM 7.7.0.  But now energy minimization fails because an old problem where OpenMM changes the default text encoding from utf-8 to ascii breaks all Google Colab shell magic has returned.  ChimeraX uses the Google Colab shell magic (e.g. ""!zip -r results.zip ..."").  I had a work-around in the code to fix the text encoding but it is no longer working with Python 3.10 and the updated OpenMM 7.7.0.  I need to figure out a new fix so that OpenMM does not change the text encoding.

In the meantime I changed the ChimeraX AlphaFold script so it warns that energy minimization is not available, and it predicts with no energy minimization even if minimization was requested."	defect	closed	high		Structure Prediction		fixed						all	ChimeraX