traning problem

[maxshen29]

i use the sample ：

from igfold import IgFoldRunner sequences = { "H": "QVQLQESGGGLVQAGGSLTLSCAVSGLTFSNYAMGWFRQAPGKEREFVAAITWDGGNTYYTDSVKGRFTISRDNAKNTVFLQMNSLKPEDTAVYYCAAKLLGSSRYELALAGYDYWGQGTQVTVS" } pred_pdb = "my_nanobody.pdb"

igfold = IgFoldRunner() igfold.fold( pred_pdb, # Output PDB file sequences=sequences, # Nanobody sequence do_refine=False, # Refine the antibody structure with PyRosetta do_renum=True, # Renumber predicted antibody structure (Chothia) )

get the erro： Warning: AbNumber not available. Provide --use_abnum to renumber with the AbNum server. cannot import name 'clean_pdb' from 'igfold.utils.pdb' (/data/miniconda3/envs/igfold/lib/python3.9/site-packages/igfold/utils/pdb.py) Completed folding in 0.90 seconds.

How to solve it？

[jeffreyruffolo]

Hello, I recently replaced ANARCI with AbNumber for renumbering structures. You may need to install this tool specifically, here's the conda command:

$ conda install -c bioconda abnumber

Altnernatively, you can pass the use_abnum=True argument to the igfold.fold command, which will send your structure to a server for renumbering.

[kimdn]

Both my python3.8 and 3.9 condas cannot install abnumber as

My python3.7 conda local environment cannot install abnumber as well as

Maybe I just need to use

igfold.fold(
pred_pdb, # Output PDB file
sequences=sequences, # Nanobody sequence
do_refine=False, # Refine the antibody structure with PyRosetta
do_renum=True, # Renumber predicted antibody structure (Chothia)
use_abnum=True,
)