RosettaCommons / RosettaCommons/RFdiffusion

Why does the output PDB designs only contain Glycines??

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Python
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Description

Hello,

Thank you for creating this wonderful software; I foresee great success!
I am trying to run a simple unconditional monomer from my PDB file using the README.md tutorials. So I have my environment set up and the PDB file (an AAV monomer) in the path I want it, this is my command:

(SE3nv) C:\my\Path\RFdiffusion>python .\scripts\run_inference.py "contigmap.contigs=[534-534]" inference.input_pdb=C:\my\Path\RFdiffusion\sample.pdb inference.output_prefix=test_outputs\test inference.num_designs=10

When I run this, all 10 designs come out with a sequence of only Glycine and do not look anything like an AAV monomer. What am I doing wrong or not understanding? Please help me understand.

Thanks,

Heather

Also, disclosure: I am relatively new to computer science and not an avid coder, so please be gentle and break down explanations if possible.

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Research direction

Start with the README.md tutorials and the command invoking scripts/run_inference.py, then reproduce the result using sample.pdb and the stated contigmap.contigs setting. Trace how the input PDB and output sequences are handled; done means identifying whether the Glycine-only designs result from usage, input interpretation, or a software defect and documenting the finding.

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Assessment

Tech stack
python
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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