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Please guide me with this error. Please!
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/5jqwA/…
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Hi,
I have noticed that the information in the datasets' .csv files columns does not always match the information in the raw PDB files'.
I suspect there is some non-obvious shifting being applied …
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After processing some PDB files from [PINDER](https://github.com/pinder-org/pinder) with `process_pdb_files.py` when running the training I get
```
python -W ignore experiments/train_se3_flows.py da…
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pdbs in platinum and pdbbind have missing amino acids and so our datasets are smaller than they should be since we ignore those pdbs.
Need to get their sequences from fasta files from PDB
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Hello,
Thanks for the great work! I tried your method for training 4D scenes using the monocular videos of Davis-2016 dataset (I only tested the Bear scene). However, the loss became NaN at epoch 2…
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Hi I'm interested in your research, and I want to do further experiments. Could you share your full backrub pdb datasets for s2003? I tried to make complex using rosetta, but there are many failure ca…
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Hi,
Great work and thanks for uploading the raw data! I followed the instruction to preprocess the raw data, however I get the following errors. Does this error matter for the training process?
T…
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Hello, when running classification task on go-bp dataset, it gives an error:
FileNotFoundError: 4v8m not found in raw directory. Are you sure it's downloaded and has the format pdb?
with the for…
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Hi,
I'm using Graphein on Google Colab, I have a list of PDB ids `pdb_ids` and I'm using `ProteinGraphDataset(...)` to create a dataset.
```
!pip install graphein[extras] torch-geometric
```
```
…
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pdbfixer adds four hydrogens to the N of the CASN, which is undoubtedly wrong, but the program does not report an error. when I input this structure into openmm to minimize it, the program shows the m…