AssertionError: ('B', 1) is not in pdb file!

[alymakhlouf]

Hello,

I keep trying to run the binder design example: ./scripts/run_inference.py 'contigmap.contigs=[B1-100/0 100-100]' inference.output_prefix=test_outputs/binder_test inference.num_designs=10

But there seems to be an issue with how the PDB files are being read. I keep getting the following error: "AssertionError: ('B', 1) is not in pdb file!". This is irrespective of which PDB file I specify from the 'input_pdbs' folder, or whether I even specify an 'inference.input_pdb' argument at all. Could you please help with this?

Thanks

[atumbio]

So I did the same thing trying to run run_inference.py but that is just a starting point that will allow you to customize what you want to target. What you'll want to run is:

An example of binder design with RFdiffusion can be found in ./examples/design_ppi.sh

It's in the docs and in that script, you'll see how you can run run_inference.py to your liking

[polymerase60053]

RFdiffusion will re-order chains, you can try 'contigmap.contigs=[100-100/0 B1-100]'
See #214 and #282

[alymakhlouf]

Thank you both for your replies. So I've done some digging and found that when I run the parsed_pdb function on '1qys.pdb' (one of the structures in the examples/input_pdbs directory) and get the 'pdb_idx', there is no B1. In fact there doesn't seem to be a B chain in any of the structures listed in the input_pdbs folder, and I've even tried uploading a separate structure that I downloaded myself and it also doesn't have a B chain. All of the structures seem to have truncated A chains, for example A3-36, A38-A100 etc. I'm new to this so I was a bit surprised to see it, but looking at some of the structures on rcsb.org seems to confirm that this is just how they've been deposited.

Thanks

[polymerase60053]

It's normal for pdbs to have no B chain and not start from A1. You can either find a pdb with B1-100 in it or follow atumbio's advice to run official examples first.

[alymakhlouf]

Good to know. Now that I know how to access this information about the chain before running the script I can just adjust contigmap.contigs accordingly.

Thanks a lot for your help