Skip to content

Urgent: Unable to load custom PDB RFDiffusion #190

@sbhakat

Description

@sbhakat

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?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions