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jwohlwend / boltz

Official repository for the Boltz-1 biomolecular interaction model
MIT License
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Suggestions for Enhancements to Colab Notebook for Boltz-1 Inference #28

Open thisisanshgupta opened 3 days ago

thisisanshgupta commented 3 days ago

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 commented 3 days ago

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

LJStewart5 commented 2 days ago

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 commented 2 days ago

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

thisisanshgupta commented 2 days ago

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

Jun-Lizst commented 2 days ago

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 commented 1 day ago

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 commented 22 hours ago

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 commented 20 hours ago

Weixin Screenshot_20241122190250 Hello, I encounter a new bug, I can not find cif file in the output. Thanks!

Jun-Lizst commented 20 hours ago

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 commented 19 hours ago

image Major error reported.