Results with custom MSA are different and misfolded compared to the result from --use_msa_server

[kartik-rallapalli]

I am trying to fold a protein+RNA structure and while the predict fold is correct in case of the server generated MSAs (screenshot with green ribbons)(

), when I try to predict the same complex with a custom MSA the RNA fold seems distorted(orange in the screenshot

). Intriguingly, the custom MSA used in this case is the output generated from the --use-msa-server. Has anyone encountered/resolved such a issue yet? Thank you!

[wehs7661]

Sorry I am not sure how to resolve this issue but I wonder what MSA file you used from the case where --use-msa-server. Did you use bfd*.a3m or uniref.a3m in the output msa folder? Thanks a lot!