During run Prediction

[cjwilli98]

Expected Behavior

Current Behavior

ModuleNotFoundError Traceback (most recent call last) in <cell line: 65>() 63 64 download_alphafold_params(model_type, Path(".")) ---> 65 results = run( 66 queries=queries, 67 result_dir=result_dir,

5 frames /content/alphafold/relax/cleanup.py in 20 import io 21 ---> 22 import pdbfixer 23 from openmm import app 24 from openmm.app import element

ModuleNotFoundError: No module named 'pdbfixer'

---

NOTE: If your import is failing due to a missing package, you can manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the "Open Examples" button below

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab. If running locally ypdate you local installation colabfold_batch to the newest version. Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used
• If you run it on a local system. Please add the server specifications
• Operating system and version:

[cjwilli98]

!pip install pdfminer import pdfminer print("pdfminer is installed and ready to use") output:ModuleNotFoundError Traceback (most recent call last) in <cell line: 1>() ----> 1 import pdfminer 2 print("pdfminer is installed and ready to use")

ModuleNotFoundError: No module named 'pdfminer'

---

NOTE: If your import is failing due to a missing package, you can manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the "Open Examples" button below. ------------------------------------- So I have the issue running the program and then trying to manually install the package

[milot-mirdita]

Which notebook is this?