openfold usage error

[Xinheng-He]

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]

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]

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]

Hi Xinheng,

Thanks for pointing that out. Alternatively, you can also comment out the models/finetuning_ptm_2.pt loading code located at

MutateEverything/modeling/backbone.py

Line 56 in c380ea9

ckpt = torch.load(self.args.finetune_backbone, map_location='cpu')

MutateEverything/modeling/backbone.py

Line 57 in c380ea9

self.backbone.load_state_dict(ckpt, strict=False)

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?