search

baker-laboratory / RoseTTAFold-All-Atom

Other
652 stars 118 forks source link

protein ssDNA complex gives overlapped structure result #136

Open fglaser opened 3 months ago

fglaser commented 3 months ago

Hi, I run a protein-ssDNA complex and got a result without errors, but the pdb shows a non-physical overlap between them. I wonder if this is a RFAA problem, or something else you may have spotted before.

I paste the inputs and the pdb (as .pdp.txt). Thanks a lot in advance, Fabian

more rf2aa/config/inference/RFA2_HUMAN_ssDNA.yaml defaults:

job_name: "RFA2_HUMAN.ssDNA" protein_inputs: A: fasta_file: examples/all/RFA2_HUMAN.fasta na_inputs: B: fasta: examples/all/RFA2_HUMAN.ssDNA.fasta input_type: "dna"

loader_params: MAXCYCLE: 10

:::::::::::::: examples/all/RFA2_HUMAN.fasta ::::::::::::::

RFA2_HUMAN MWNSGFESYGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYV KVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNE GHIYSTVDDDHFKSTDAE :::::::::::::: examples/all/RFA2_HUMAN.ssDNA.fasta :::::::::::::: ssDNA_RFA2_HUMAN TTAGGG

RFA2_HUMAN.ssDNA.relaxed.pdb.txt