Error in Prediction of RNA structure with Protein

[didEldi]

I tried to predict two RNA strands with cas9 (PDB ID: 4OO8).
However, RNA structures were crashed like fragment of skein.
Not only for this, but also same RNA structure were simulated without protein.
Overall structure was good but there is a disconnection in single strand.
I wonder if this is normally happen in this prediction or there are some problems in my simulation.

[anar-rzayev]

Hello, thanks for your issue. I am trying to experiment with different Cas9 protein structures, and I stumbled upon your problem here. Can I know which exactly .fa files are you running? I am a bit confused because there are 3 possible sequences, and running altogether in separate files somehow gave me memory issues i dunno why

[anar-rzayev]

@didEldi Just for reference, I recently ran the RF2NA model with my redesigned sequence, RNA, and DNA strand of the 4OO8 SpCas9 complex and got the following results:

../run_RF2NA.sh success P:cas9_chain_A_10.fa R:cas9_rna.fa D:cas9_dna.fa

Running on GPU
           plddt    best
RECYCLE  0   0.646  -1.000
RECYCLE  1   0.706   0.646
RECYCLE  2   0.726   0.706
RECYCLE  3   0.720   0.726
RECYCLE  4   0.720   0.726
RECYCLE  5   0.709   0.726
RECYCLE  6   0.706   0.726
RECYCLE  7   0.712   0.726
RECYCLE  8   0.708   0.726
RECYCLE  9   0.706   0.726
Done

What do you think about this structure result?