sokrypton
MPNN designed sequence not separated correctly with multiple targets and multiple binders
With a toy example, my contig string is 'A 20 E 10' with a modified pdb structure. The output sequence is: TTCCPSIRSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN/RRRNNDKPVDMLYPMVAMEMTLGSEFEVME
In the above output, the two target sequences (chain A and E) are combined, followed by "/", then followed by two binder sequences (20 + 10). There is no separation "/" between the two targets and the two binders.
Some initial tracing of the code points to line 27 in af.prep._prep_binder
self._lengths = [self._target_len, self._binder_len]
self._lengths only contain two elements. This is later passed on to the mpnn code, leading to mpnn think there are only two chains in sequence output. I can certainly read the sequences from the final PDB file, just wonder if this is something that needs to be fixed.
Thanks!
This shouldn't affect the results. but I'll make some edits so that the chains are printed as separate chains.
Thanks!
On Sat, May 13, 2023, 1:44 AM Yingyao Zhou @.***> wrote:
With a toy example, my contig string is 'A 20 E 10' with a modified pdb structure. The output sequence is: TTCCPSIRSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN/RRRNNDKPVDMLYPMVAMEMTLGSEFEVME
In the above output, the two target sequences (chain A and E) are combined, followed by "/", then followed by two binder sequences (20 + 10). There is no separation "/" between the two targets and the two binders.
Some initial tracing of the code points to line 27 in af.prep._prep_binder
self._lengths = [self._target_len, self._binder_len]
self._lengths only contain two elements. This is later passed on to the mpnn code, leading to mpnn think there are only two chains in sequence output. I can certainly read the sequences from the final PDB file, just wonder if this is something that needs to be fixed.
Thanks!
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