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jozhang97 / MutateEverything

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openfold usage error #10

Open Xinheng-He opened 2 months ago

Xinheng-He commented 2 months ago

image Dear developers, I'm trying to use this package to do mutation and I've followed the install protocol. However, I meet this problem. I also found that in the openfold folder, no subfolder called data exists. Is there any solution? Thanks.

jozhang97 commented 2 months ago

Hi, sorry to hear about this issue. It turns out that I gitignored any data files.

I've updated the repo, Can you try reinstalling openfold? Something like this (or a clean restart might be better)

git pull origin master
pip uninstall openfold
cd openfold
python3 setup.py install
cd ..
Xinheng-He commented 2 months ago

Thanks for your reply and currently it works. I still want to remind that if runing alphafold test protocol, it needs models/finetuning_ptm_2.pt. In the previous readme. md, such files only need to be downloaded during re-training. Maybe you can also remind the test users to download the .pt from openfold. That's an amazing program and thanks again for your development.

jozhang97 commented 1 month ago

Hi Xinheng,

Thanks for pointing that out. Alternatively, you can also comment out the models/finetuning_ptm_2.pt loading code located at https://github.com/jozhang97/MutateEverything/blob/c380ea9fa185b770df25127e8aabbccbd212a074/modeling/backbone.py#L56 https://github.com/jozhang97/MutateEverything/blob/c380ea9fa185b770df25127e8aabbccbd212a074/modeling/backbone.py#L57

I agree I should remind the users about this. Let me think what's the easiest way to do this.

Additionally, I updated the model checkpoint at https://utexas.box.com/s/y0hklxvgqt515pkztb305qnibcv0l0tq that fixed a small bug (README.md is up to date now). Were you able to use the latest one?