Hello,
I am using PIPPack for a large scale project and I noticed that a small fraction of my proteins were shorter by one residue after side-chain packing. I checked those backbone pdbs are those seemed to be valid structures. The issue turned out to be the line from inference.py:
atom_mask = (np.sum(atom_positions, axis=-1) != 0.0).astype(np.int32)
I suppose this is a check for placeholder coordinates that are all zero, but in reality some coordinates will sum to zero just by chance, causing the pipeline to drop this position.
You count instead explicitly check for all zero positions, or additionally, consider the "occupancy" column to be 0 as well. Unless of course there is a reason for the sum != 0.0 check.
Thank you,
Filip
Hello,
I am using PIPPack for a large scale project and I noticed that a small fraction of my proteins were shorter by one residue after side-chain packing. I checked those backbone pdbs are those seemed to be valid structures. The issue turned out to be the line from inference.py:
atom_mask = (np.sum(atom_positions, axis=-1) != 0.0).astype(np.int32)I suppose this is a check for placeholder coordinates that are all zero, but in reality some coordinates will sum to zero just by chance, causing the pipeline to drop this position.
You count instead explicitly check for all zero positions, or additionally, consider the "occupancy" column to be 0 as well. Unless of course there is a reason for the sum != 0.0 check.
Thank you,
Filip