images of structures not rendering in jupyter

[lauradunphy]

Hello,

Thanks for creating this great tool! When I run output.ipynb, the figures from parse_results_colour_chains and parse_results do not render in either VSCode or Jupyter notebook. I do get text in the below format when I run the cells, however no images are displayed. display_pae_plots renders just fine. I tried just utilizing py3Dmol outside of your function and appear to have the same issue. Do you need to install any additional dependencies or extensions to visualize the results of py3Dmol?

 ==> Parsing a PDB/mmCIF file: $PATH/ranked_0.pdb
 ==> Parsing a PDB/mmCIF file: $PATH/ranked_1.pdb
 ==> Parsing a PDB/mmCIF file: $PATH/ranked_2.pdb
 ==> Parsing a PDB/mmCIF file: $PATH/ranked_3.pdb
 ==> Parsing a PDB/mmCIF file: $PATH/ranked_4.pdb

Many thanks,
Laura

[dingquanyu]

Hi Laura,

Sorry it seems other users have also reported the same issue with displaying the 3D models recently and I'm looking into it right now and aim to get back to you later.

Cheers

[dingquanyu]

Hi @lauradunphy

It turned out that the issue came from the outdated py3Dmol package. Could you please, within the same conda env you created for AlphaPulldown, run pip install py3Dmol==2.0.1 then jupyter-lab. I have tried it myself and it works now with updated py3Dmol.

Please let me know if this solution also works for you and leave the issue open just in case other users may have the same problem.

Yours
Dingquan

[lauradunphy]

Hi Dingquan,

Updating the pyD3mol package also worked for me! Thanks so much

Many thanks,
Laura