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Rappsilber-Laboratory / AlphaLink2

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer
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distance_distribution, pae, plddt not in output directory #29

Closed adahal258 closed 3 months ago

adahal258 commented 3 months ago

Does alphalink2 installed on local device creates .svg files for distance_distribution, pae and plddt. I am not getting these files in my output directory. Also, attached is the output I get, is it something with CUDA or openmm Capture

Thank You!

lhatsk commented 3 months ago

No, it's only part of ColabFold.

You can ignore the warning. We don't use jaxlib, it just comes with AlphaFold.

jimfeng9705 commented 3 months ago

How can we obtain a json file that contains plddt (scores)? We would like to use the scores file and the pdb to view the predictions, using, e.g., PAE Viewer?

jimfeng9705 commented 3 months ago

Is it possible to generate the predicted LDDT images as we see on the colab site? See attached pictures. download

lhatsk commented 3 months ago

The json files should be present in the output directory. I'm not sure if they have the same format as the AlphaFold score files though. The PAE viewer looks cool! You might need to change the format of the crosslinks if you want to show them.

You could generate the plots if you import colab_plot_confidence from unifold/colab/plot.py see https://github.com/Rappsilber-Laboratory/AlphaLink2/blob/main/unifold/colab/plot.py#L114

Maybe I will add it later.