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Urgent: Unable to load custom PDB RFDiffusion

Open sbhakat opened this issue 11 months ago • 0 comments

I am trying to upload the PDB (link: https://www.dropbox.com/s/koxlbk5ntgzzlv6/protchain1.pdb?dl=0) which only has chain A in the RF Diffusion Colab but I am getting the following error:

7ki0.pdb(chemical/x-pdb) - 264951 bytes, last modified: n/a - 0% done
 ---------------------------------------------------------------------------
MessageError                              Traceback (most recent call last)
<timed exec> in <module>

<timed exec> in run_diffusion(contigs, path, pdb, iterations, symmetry, order, hotspot, chains, add_potential, partial_T, num_designs, use_beta_model, visual)

<timed exec> in get_pdb(pdb_code)

[/usr/local/lib/python3.11/dist-packages/google/colab/files.py](https://lkvs0bt85ys-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab_20250206-060131_RC00_723872503#) in upload(target_dir)
     70   """
     71 
---> 72   uploaded_files = _upload_files(multiple=True)
     73   # Mapping from original filename to filename as saved locally.
     74   local_filenames = dict()

2 frames
[/usr/local/lib/python3.11/dist-packages/google/colab/_message.py](https://lkvs0bt85ys-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab_20250206-060131_RC00_723872503#) in read_reply_from_input(message_id, timeout_sec)
    101     ):
    102       if 'error' in reply:
--> 103         raise MessageError(reply['error'])
    104       return reply.get('data', None)
    105 

MessageError: RangeError: Maximum call stack size exceeded.

The code-snippet corresponding the selection is following

contigs = "A:30" #@param {type:"string"}
pdb = "" #@param {type:"string"}

I am really stuck, any help to debug this error will be highly appreciated?

sbhakat avatar Feb 10 '25 00:02 sbhakat