Changes between Initial Version and Version 4 of Ticket #8182

Timestamp:

May 10, 2023, 12:07:55 AM (2 years ago)

Author:

Tom Goddard

Comment:

Done.

I updated about 3 weeks ago to use the newer ColabFold and no changes were needed. I was forced to do this update because Google Colab updated to Python 3.10 (unannounced) and broke ColabFold because it relied on an older tensorflow package that was not available in 3.10. Unfortunately the Python 3.10 update also broke OpenMM installation so energy minimization with AlphaFold is broken. Although ColabFold fixed this by updating to OpenMM 7.7.0 (from 7.5.1) it is still broken in ChimeraX because the new OpenMM changes the preferred text encoding to ascii from utf-8 breaking all Google Colab shell magic which ColabFold does not use but ChimeraX does. I had a work-around to fix the text encoding change caused by OpenMM that no longer works after the update from Python 3.9 / OpenMM 7.5.1 to Python 3.10 / OpenMM 7.7.0. There is a separate ticket to fix this problem #8975.