Check out their github and see if someone already had such issue and received an answer from the authors. Otherwise, you can report the issue (in github also)..
Yesterday I used this notebook and it worked fine.
The Alphafold tool is a deep learning-based protein folding prediction tool, and it typically outputs a predicted 3D structure in PDB format. If you are not getting the output in PDB format, there could be several reasons for this:
Input format: Alphafold requires the input sequence in fasta format, so make sure that your input sequence is in this format.
Output format: Alphafold provides the output in PDB format, but you may need to specify this format in your parameters or options. Check the documentation or the command line options for Alphafold to see if you need to specify the output format.
Version compatibility: Make sure that you are using the latest version of Alphafold and that it is compatible with your operating system.
Internet connectivity: Alphafold requires an internet connection to run, so make sure that your computer is connected to the internet and that you have access to the Alphafold server.
Data availability: Alphafold uses a deep learning model that has been trained on a large dataset of proteins, so it may not be able to predict the structure of every protein. If your protein is not in the training dataset, the predictions may not be accurate.
If you have tried these steps and you are still not getting the output in PDB format, you may want to contact the Alphafold support team for further assistance. They may be able to provide additional information or help you troubleshoot the issue.
I had a similar issue. Are you getting PDF files as well? Because Adobe is one of the main programs on my computer and I could find out that the .pdb files were considered to be a PDF and opened with it. But when you choose to open with Chimera it works.