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nrbennet / dl_binder_design

MIT License
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Issue with silent file index #7

Closed arikat closed 1 year ago

arikat commented 1 year ago

Hi! Using this as part of the RFdiffusion protocol. Currently running into the following error when MPNN is being used when running dl_binder_design.py:

core.io.silent.SilentFileData: Finished reading 1 structures from temp.silent
No GPU found, running MPNN on CPU
Attempting pose: temp
Traceback (most recent call last):
File "/home/user/Software/dl_binder_design/mpnn_fr/dl_interface_design.py", line 226, in main( pdb, silent_structure, mpnn_model, sfd_in, sfd_out )
File "/home/user/Software/dl_binder_design/mpnn_fr/dl_interface_design.py", line 169, in main dl_design( pose, pdb, silent_structure, mpnn_model, sfd_out )
File "/home/user/Software/dl_binder_design/mpnn_fr/dl_interface_design.py", line 133, in dl_design chains = get_chains( pose )
File "/home/user/Software/dl_binder_design/mpnn_fr/dl_interface_design.py", line 114, in get_chains endB = endA + pose.split_by_chain()[2].size()

IndexError

I assume it's having some problem reading my silent file? Is there an example silent file I could use to test if it's my silent file or possibly an issue with my environment?

nrbennet commented 1 year ago

This issue is due to your silent file having a structure containing only 1 chain and not 2.

You can run silentextract to take that silent file to a bunch of pdbs and take a look at them.

arikat commented 1 year ago

Thank you so much! You were right, my output from RF diffusion had chain A (binder) and chain B (protein) concatenated for some reason. I just fixed that by separating them back into two chains and everything worked as expected. Thank you again!