[chimerax-users] Error reported by AlphaFold

[Juntao Yu]

Dear ChimeraX community,

I am a graduate student from Harvard Medical School who recently became interested in using AlphaFold-Multimer to predict protein complex structures of my interest. I have been tried a few times of predicting one protein complex and I was able to finish all MSA. However, when AlphaFold starts predicting the structure, all five models were reported as “error”. It is surprising to me because it is known that these two proteins should form a complex. I noticed in the script on the line is: “print ('\nAlphaFold generated an error computing %s, error logged to %s\n'% (model_name, error_log_path))”. The results printed exactly what this line says. 

I am wondering whether it means the Multimer is not able to predict this complex structure? Is there any tutorial that I can find to change parameters in order to try to improve and get a structure?

Thanks,
Juntao

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Juntao Yu | Ph.D. candidate
Moazed Lab
Department of Cell Biology
Harvard Medical School
240 Longwood Avenue
Boston, MA 02115

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