problem accessing coordinates of antigen for RabD

[yogeshverma1998]

Hi,

I am trying to download the RabD dataset via the summary file and it created an JSON file. However, the entries of the JSON file are:
{'pdb': '5nuz', 'heavy_chain': 'A', 'light_chain': 'B', 'antigen_chains': ['C'], 'pdb_data_path': '5nuz.pdb', 'numbering': 'imgt', 'pre_numbered': False, 'heavy_chain_seq': 'EVQLQQSGTVLARPGASVKMSCKASGYTFTSYWMHWIKQRPGQGLEWIGAIYPGDSDTKYNQKFKGKAKLTAVTSTSTAYMELSSLTNEDSAVYYCTRRNTLTGDYFDYWGQGTTLTVSS', 'light_chain_seq': 'DIVLTQSPASLAVSLGQRATISCRASESVDDYGISFMNWFQQKPGQPPKLLIYTASSQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPYTFGGGTKLEIK', 'antigen_seqs': ['LPLLCTLNKSHLYIKGGNASFQISFDDIAVLLPQYDVIIQHPADMSWCSKSDDQIWLSQWFMNAVGHDWHLDPPFLCRNRTKTEGFIFQVNTSKTGVNENYAKKFKTGMHHLYREYPDSCLNGKLCLMKAQPTSWPLQCPLD'], 'cdrh1_pos': (25, 32), 'cdrh1_seq': 'GYTFTSYW', 'cdrh2_pos': (50, 57), 'cdrh2_seq': 'IYPGDSDT', 'cdrh3_pos': (96, 108), 'cdrh3_seq': 'TRRNTLTGDYFDY', 'cdrl1_pos': (26, 35), 'cdrl1_seq': 'ESVDDYGISF', 'cdrl2_pos': (53, 55), 'cdrl2_seq': 'TAS', 'cdrl3_pos': (92, 100), 'cdrl3_seq': 'QQSKEVPYT'},
However, there are not any antigen spatial coordinates here. I think you have used the antigen coordinates for the experiment in your paper. Can you let me know if is this correct and how one can get antigen coordinates in this case?

Thanks!

[kxz18]

Hi, this is expected because this is only a summary of the dataset. You can see there is a 'pdb_data_path' key in the json, which refers to the path of the pdb data. When coordinates are needed, we will extract them from the pdb file with the Protein class or the AgAbComplex class defined in data/pdb_utils.py. Parsing coordinates from pdb files is time-consuming, so in the cases where we only want the sequence data, we can directly read them from the summary, which is more efficient.

[kxz18]

Hi, I'm wondering if the problem has been solved? If so, could you please close the issue?