Suggestions for Enhancements to Colab Notebook for Boltz-1 Inference

[thisisanshgupta]

I created a Colab notebook for running inference with the Boltz-1 model. Are there other features or functionalities you'd recommend adding to improve it?
Any suggestions are appreciated!

Thanks!

[Jun-Lizst]

I am willing to test the colab notebook for boltz-1. Thanks!

[LJStewart5]

I'm also willing to test Colab with Boltz-1 model. Is there a link to a Colab instance that I can copy and use ?

[thisisanshgupta]

Sure, I will make it available after making some tweaks and completing the code for visualizing the predicted structure.

[thisisanshgupta]

here's the Colab link:
https://colab.research.google.com/drive/1B_xSLii8ZMvp4K4XL2zslQVbKIjWV-mp?usp=sharing
Feel free to suggest necessary improvements.

[Jun-Lizst]

Thank you very much for sharing!
But I have this error: Installing collected packages: antlr4-python3-runtime, types-requests, omegaconf, numpy, mashumaro, lightning-utilities, ihm, rdkit, pandas, modelcif, hydra-core, einx, biopython, torchmetrics, fairscale, pytorch-lightning, boltz
Attempting uninstall: numpy
Found existing installation: numpy 1.26.4
Uninstalling numpy-1.26.4:
Successfully uninstalled numpy-1.26.4
Attempting uninstall: pandas
Found existing installation: pandas 2.2.2
Uninstalling pandas-2.2.2:
Successfully uninstalled pandas-2.2.2
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
cudf-cu12 24.10.1 requires pandas<2.2.3dev0,>=2.0, but you have pandas 2.2.3 which is incompatible.
google-colab 1.0.0 requires pandas==2.2.2, but you have pandas 2.2.3 which is incompatible.

[thisisanshgupta]

Thank you very much for sharing! But I have this error: Installing collected packages: antlr4-python3-runtime, types-requests, omegaconf, numpy, mashumaro, lightning-utilities, ihm, rdkit, pandas, modelcif, hydra-core, einx, biopython, torchmetrics, fairscale, pytorch-lightning, boltz Attempting uninstall: numpy Found existing installation: numpy 1.26.4 Uninstalling numpy-1.26.4: Successfully uninstalled numpy-1.26.4 Attempting uninstall: pandas Found existing installation: pandas 2.2.2 Uninstalling pandas-2.2.2: Successfully uninstalled pandas-2.2.2 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. cudf-cu12 24.10.1 requires pandas<2.2.3dev0,>=2.0, but you have pandas 2.2.3 which is incompatible. google-colab 1.0.0 requires pandas==2.2.2, but you have pandas 2.2.3 which is incompatible.

I don't think you'll be getting these errors if you're on Colab. Still you should try downgrading pandas to 2.2.2

[thisisanshgupta]

here's the Colab link: https://colab.research.google.com/drive/1B_xSLii8ZMvp4K4XL2zslQVbKIjWV-mp?usp=sharing Feel free to suggest necessary improvements.

here's an update: I added visualization for the generated sequence.

[Jun-Lizst]

Hello, I encounter a new bug, I can not find cif file in the output. Thanks!

[Jun-Lizst]

Could you please follow this notebook and also add visualizations of PAE, pLDDTs, Global confidence measures and ipTM matrix, Contact Probability Heatmap ? Thanks!
https://colab.research.google.com/drive/1XwNiH-cs4Xn5P_F5kxL78LjBoTafDErZ?usp=sharing

[Jun-Lizst]

Major error reported.