foundry

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Problem with heteroatoms

2

I am getting an error that appears to be associated with the oxygens and nitrogens in my .pdb file, which contains only a small molecule ligand. I haven't included the...

harris-davis

RFD3 fail to recognize ligand name, and replace the three letter ligand name into ALA after inference

2

Hi the creators of RFD3! I named my ligand as LIG in input.pdb, but it reported as: ValueError: Transforms failed at stage `CreateDesignReferenceFeatures`: could not broadcast input array from shape...

wkai24213-source

Project root directory not found

2

Hi I managed to install foundry using apptainer. RFD is working but RF is giving error FileNotFoundError: Project root directory not found. Indicators: ['.project-root']. is there a way to fix...

dhiraj82

rf3 produced very different ipTM with or without MSA specified for the test example 5vht

2

For the test example 5vht, when running rf3 prediction from the json file with MSA specified or the cif file, i got ipTM of 0.90 ; however, when I ran...

HanLab-OSU

hydrogen atoms in protein-small molecule design example

1

Hi, Thanks for releasing this amazing tool! Upon running the small-molecule binder examples against the ligand IAI, I received the following warning: > WARNING atomworks.io: We can't fix formal charges...

Feanor007

During training, why do we always set example = batch[0] for 1 instance of structure prediction? https://github.com/RosettaCommons/foundry/blob/676b4a95f3dda7f599ce2c0618033251cc4a170c/models/rfd3/src/rfd3/trainer/rfd3.py#L157

wiwnopgm

How to generation many seq in one backbone

3

hello, nice work. when i use it to design protein binder, I find it had generate sequence not GGGG...... Is it necessary to continue executing ProteinMPNN for sequence generation as...

didiwei1987

Scaffolded diffusion in rfd3

2

Hi there. Happy to see the new version. I was mostly working with the original rfdiffusion and really enjoyed the feature to provide a target pdb to guide diffusion towards...

Cookiemaster33

out of memory

2

I am trying to design binders (80-160 res.) against my protein (~650 AA) but often getting this error. I have 46 GB memory / gpu and sometime its happening that...

dhiraj82

Getting FileNotFoundError: [Errno 2] No such file or directory: '/tmp/repo/models/rfd3/configs/datasets/val/benchmarks' Replacing the dead symlink with an empty dir allows install to proceed

puddleglum56