alphafold outputs only have msas

[zsxzs]

alphafold outputs dont have features.pkl ranked_{0,1,2,3,4}.pdb ranking_debug.json relax_metrics.json relaxed_model_{1,2,3,4,5}.pdb result_model_{1,2,3,4,5}.pkl timings.json unrelaxed_model_{1,2,3,4,5}.pdb

how to fix this problem? anyone can help me? Thank you.

[yamule]

It seems that the MSA is too large. How about using --reduced_dbs option?

[sappigekip]

I have the exact same issue. using the reduced dbs option worked, and now i get all the outputs. but does anyone have an idea on how to get all the outputs with the full dbs? can we limit the MSA in the commands or something?

[tcoates5]

Based on the last dive I did, titin seemed to be causing the issues. One option would be to remove it from the database.

[sappigekip]

I see, then perhaps another question. how do i remove it from the database?