Hi, I have a complex that I made by re-folding the 6bdz sequence (which is part of your test set). The antigen-antibody pose is badly docked and I thought it could be fixed with this abdockgen repo.
I processed the pdb file into a json by doing python process_data.py ./af2_6bdz.pdb B C (and saved the processed file to ./processed/af2_6bdz.json)
And then did inference by doing python predict.py ckpts/HERN_dock.ckpt ./processed/af2_6bdz.json and the output pdb file is stored in /outputs/.
The problem is that the output file only contains the antigen and it is positioned exactly identically to how it was in the input file. So basically abdockgen's predict did absolutely nothing. If you overlay the output file onto the original, the antigen takes the exact same position.
Hi, I have a complex that I made by re-folding the 6bdz sequence (which is part of your test set). The antigen-antibody pose is badly docked and I thought it could be fixed with this abdockgen repo.
I processed the pdb file into a json by doing
python process_data.py ./af2_6bdz.pdb B C(and saved the processed file to./processed/af2_6bdz.json)And then did inference by doing
python predict.py ckpts/HERN_dock.ckpt ./processed/af2_6bdz.jsonand the output pdb file is stored in/outputs/.The problem is that the output file only contains the antigen and it is positioned exactly identically to how it was in the input file. So basically abdockgen's predict did absolutely nothing. If you overlay the output file onto the original, the antigen takes the exact same position.
Am I doing something wrong?