Reproducing dyMEAN model in Fig. 4

[bud-graziano]

Hi, great work!

I was trying to reproduce the dyMEAN model for PDB-ID 1ic7 as shown in Figure 4.

However, the models I get do not seem to be positioned as well as shown in the Figure. See the image below with green = ground truth and pink = dyMEAN model

I was wondering if you would mind sharing the settings to reproduce the model shown in the Figure? I tried to follow the examples from the README but possibly I made a mistake there. I used the api/design.py script with the following parameters:

{'model': {'checkpoint': './checkpoints/cdrh3_design.ckpt'},
 'Interface': {'pdb': './test/1ic7.pdb',
  'receptor': 'Y',
  'ligand': 'H',
  'k': 48,
  'out': './test/epitope_1ic7.json'},
 'Design': {'root_pdb_dir': './test',
  'pdbs': '1ic7.pdb',
  'epitope_defs': './test/epitope_1ic7.json',
  'heavy_chain': 'DVQLQESGPSLVKPSQTLSLTCSVTGDSITSAYWSWIRKFPGNRLEYMGYVSYSGSTYYNPSLKSRISITRDTSKNQYYLDLNSVTTEDTATYYCANWAGDYWGQGTLVTVSAA',
  'light_chain': 'DIVLTQSPATLSVTPGNSVSLSCRASQSIGNNLHWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIK',
  'out': './test',
  'suffix': 'antibody',
  'remove_chains': 'HL',
  'enable_openmm_relax': True,
  'auto_detect_cdrs': True}}