Ajasja Ljubetič

Wow, that is some elegant python code! I would recommend adding a `renumber_residues` method to biopandas. I would expect this is a common enough operation. Form completeness I would also...

The GPU memory is usually the problem. You probably got a card with too little GPU ram. You can run it on pure CPU it will just take a lot...

I guess there was an attempt at that here by @sokrypton: https://github.com/sokrypton/ColabFold/blob/main/beta/alphafold_output_at_each_recycle.ipynb

@martin-steinegger I'm having the exact same problem. No combination of quotes and escaping works: ```colabfold_batch: error: argument --msa-mode: invalid choice: 'MMseqs2' (choose from 'MMseqs2 (UniRef+Environmental)', 'MMseqs2 (UniRef only)', 'single_sequence')``` Input...

That's a good idea! (When using colab_batch specifying options with spaces makes things harder.

The bond you see is just clashing. If you use amber to relax the clashes, then this artifact will go away. That said AF2 is not sensitive to single point...

That's still a hard problem, but maybe something like: https://pubs.acs.org/doi/10.1021/acs.jpcb.7b11367

@martin-steinegger I think there should be a case to handle the single sequence mode of paired and unpaired here: https://github.com/sokrypton/ColabFold/blob/f3f924e4d0acc69ebab7083ca895339976e57f12/colabfold/batch.py#L669

And running with `--msa-mode single_sequence --pair-mode unpaired ` returns ```python 2022-04-14 17:56:17,482 Query 1/1: nLuc-ABC_B-cLuc (length 154) 2022-04-14 17:56:17,486 Could not generate input features nLuc-ABC_B-cLuc: 'NoneType' object is not subscriptable...

I'll guess I can get arounds this by making a paired+unpaired a3m my self? (I'm just not sure how a custom a3m alignment is passed down) (@sokrypton)