Installation location of utils in colabfold-conda

[baba-hashimoto]

Thank you for developing such a wonderful program. I tried to install it to reproduce it, but I didn't understand how to handle the utils folder. It may not work just by moving the folder. If there was someone who had previously succeeded in running it, I would be happy if you could share the information.

[YanapatJ]

I just replaced the original alphafold, colabfold, and utils folders in /localcolabfold/colabfold-conda/lib/python3.10/site-packages/ with the ones from Highfold, and it works for me.

[YanapatJ]

However, I am not 100% sure if that's the right way to do it or not.

[baba-hashimoto]

Thanks for your answer. I was hesitant to copy it because there was no utils in /localcolabfold/colabfold-conda/lib/python3.10/site-packages/. After copying it, I fixed some bugs (importing PDBData as SCOPData from Bio.Data) and it started working. On the other hand, I ran the following, but the peptides did not take a cyclic structure.

fasta SAKIDNLD: SSPGIWLDCTHLEGKVILVAVHVASGYIEAVIPAETGQETAYFLLLAGRWPVKTHDNGSNFTSTTVKAACWWAGIQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVIIATDIQ: SSPGIWLDCTHLEGKVILVAVHVASGYIEAVIPAETGQETAYFLLLAGRWPVKTHDNGSNFTSTTVKAACWWAGIQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVIIATDIQ

Have you created a ring structure in your calculations?

[YanapatJ]

I haven't tried that. I only did fasta

1 XXXXXX

and it works

[baba-hashimoto]

Thank you for your reply. When I ran it with the same input file, I got the following error.

2024-11-06 11:54:41,499 reranking models by 'plddt' metric 2024-11-06 11:54:41,552 Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. Traceback (most recent call last): File “/home/localcolabfold/localcolabfold/colabfold-conda/bin/colabfold_batch”, line 8, in sys.exit(main()) File “/home/localcolabfold/localcolabfold/HighFold/colabfold/batch.py”, line 2044, in main run( File “/home/localcolabfold/localcolabfold/HighFold/colabfold/batch.py”, line 1716, in run results = predict_structure( File “/home/localcolabfold/localcolabfold/HighFold/colabfold/batch.py”, line 584, in predict_structure pdb_lines = relax_me(pdb_lines=unrelaxed_pdb_lines[key], use_gpu=use_gpu_relax) File “/home/localcolabfold/localcolabfold/HighFold/colabfold/batch.py”, line 359, in relax_me relaxed_pdblines, , _ = amber_relaxer.process(prot=pdb_obj) File “/home/localcolabfold/localcolabfold/HighFold/alphafold/relax/relax.py”, line 62, in process out = amber_minimize.run_pipeline( File “/home/localcolabfold/localcolabfold/HighFold/alphafold/relax/amber_minimize.py”, line 470, in run_pipeline _check_residues_are_well_defined(prot) File “/home/localcolabfold/localcolabfold/HighFold/alphafold/relax/amber_minimize.py”, line 145, in _check_residues_are_well_defined raise ValueError("Amber minimization can only be performed on proteins with” ValueError: Amber minimization can only be performed on proteins with well-defined residues. This protein contains at least one residue with no atoms. When I ran it without --amber, it worked, but the pdb file was like the following. MODEL 1 TER 1 UNK A 6 ENDMDL END When you ran it, did it output the coordinates of some kind of cyclic peptide?

[YanapatJ]

check issue #2