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lhatsk / AlphaLink

AlphaLink: Integrating crosslinking MS data into OpenFold
Apache License 2.0
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Request for an example folder #16

Open wtq18 opened 1 year ago

wtq18 commented 1 year ago

Hi,

Is it possible to create a folder with sample files (including "7K3N_A.fasta", "restraints.csv", and "photoL.csv") as mentioned in the provided example? This would help us better understand the work and run the tool.

As shown in the examples from https://github.com/lhatsk/AlphaLink#readme: python predict_with_crosslinks.py 7K3N_A.fasta restraints.csv... python predict_with_crosslinks.py 7K3N_A.fasta photoL.csv ...

lhatsk commented 1 year ago

Hi,

Sorry for the late response! Unfortunately, that data is not public. But there is AlphaLink/test_set which has inputs that you could use for testing.

Do you have a specific question that would help you to understand the usage?

The crosslink input is essentially only a list of contacts. You can convert this list with the preprocessing_distributions.py script in case you want a distogram.