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protein ssDNA complex gives overlapped structure result #136

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fglaser opened this issue Jul 31, 2024 · 0 comments
Open

protein ssDNA complex gives overlapped structure result #136

fglaser opened this issue Jul 31, 2024 · 0 comments

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@fglaser
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fglaser commented Jul 31, 2024

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:

  • base

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

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