![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7258 closed enhancement (fixed)
Make AlphaFold prediction handle energy minimization failure
| Reported by: | Tom Goddard | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
AlphaFold prediction fails about 5% of the time with an OpenMM energy minimization failure. Sometimes it says failed to minimize in 100 steps, sometimes NaN atom coordinates. Probably this happens when AlphaFold produces bad clashes.
The ChimeraX Google Colab script should catch minimization errors, warn about it, and just return the unminimized structure.
Note:
See TracTickets
for help on using tickets.
Done.
Return unrelaxed structure prediction and warn when minimization fails.