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binbinbinv / GATSol

GATSol, an enhanced predictor of protein solubility through the synergy of 3D structure information and large language modeling
MIT License
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GATsol failed on test #2

Open ppxwwtaking opened 1 month ago

ppxwwtaking commented 1 month ago

You have two proteins examples in Predict. I assume those are your test cases, and should be well tested. However, when I run bash ./tools/Predict.sh, it failed. I checked step by step, and found the first step bash ./tools/pdb_to_cm/pdb_to_cm.sh actually requires to activate the pyg conda env, which we don't have.

I believe we should not use the shell scripts. I will try the python scripts.

ppxwwtaking commented 1 month ago

And when extracting the features, numpy possibly conflicts with matplotlib.

ppxwwtaking commented 1 month ago

After I downgrade numpy to 1.26.4, the error comes from import iFeatureOmegaCLI. I tried to pip install it, but still failed to work. So now I go to the iFeatureOmegaCLI github to get more information.

ppxwwtaking commented 1 month ago

Finally, I found it is matplotlib version issue, use 3.4.3. Problem resolved.

binbinbinv commented 1 month ago

bash ./tools/pdb_to_cm/pdb_to_cm.sh

Sorry for the delayed response, and thank you for the feedback. Are all the issues resolved now? Is the command bash ./tools/pdb_to_cm/pdb_to_cm.sh running correctly? Please let me know if there's anything else I can assist with.

ppxwwtaking commented 1 month ago

all work now. Thanks,

ppxwwtaking commented 3 weeks ago

One more question: when using GATSol for analysing antibody solubility, the fasta should include both heavy and light chains. How to put them together in one .fasta file?