bioinformatics - How do you convert a .cif file to a .mol file? - Stack Overflow

admin管理员组

文章数量:1353578

I've been working with AlphaFold 3 on a Linux HPC, and I've been trying to use Posebusters to evaluate the results of AlphaFold 3 by comparing the predicted structures with the ground truth structures from the Protein Data Bank. However, Posebusters only works with .sdf, .mol, and .mol2 files, and AlphaFold 3 outputs its predictions in a .cif file. I've been spending way too long trying to figure out how to convert a .cif file to a .mol file. I've been researching how to use OpenBabel on a Linux HPC, and I even tried to use the OpenBabel website online, but the output seems to not be good as when I tried to compare the .mol files the OpenBabel website outputted, I got this message in my terminal: Could not load molecule from 1je8-prediction.mol2 with error: 1je8-prediction.mol2 invalid_mol_at_pos_0 passes (0 / 11) Could not load molecule from 1je8-gt.mol2 with error: Could not load molecule. 1je8-gt.mol2 invalid_mol_at_pos_0 passes (0 / 11).

Does anyone know how to convert a .cif file to a .mol file effectively?

Thank you

I've been working with AlphaFold 3 on a Linux HPC, and I've been trying to use Posebusters to evaluate the results of AlphaFold 3 by comparing the predicted structures with the ground truth structures from the Protein Data Bank. However, Posebusters only works with .sdf, .mol, and .mol2 files, and AlphaFold 3 outputs its predictions in a .cif file. I've been spending way too long trying to figure out how to convert a .cif file to a .mol file. I've been researching how to use OpenBabel on a Linux HPC, and I even tried to use the OpenBabel website online, but the output seems to not be good as when I tried to compare the .mol files the OpenBabel website outputted, I got this message in my terminal: Could not load molecule from 1je8-prediction.mol2 with error: 1je8-prediction.mol2 invalid_mol_at_pos_0 passes (0 / 11) Could not load molecule from 1je8-gt.mol2 with error: Could not load molecule. 1je8-gt.mol2 invalid_mol_at_pos_0 passes (0 / 11).

Does anyone know how to convert a .cif file to a .mol file effectively?

Thank you

• file
• bioinformatics
• biopython
• file-conversion

Share Improve this question Follow asked Mar 31 at 16:26 meleemelee 11322 silver badges99 bronze badges 0

Add a comment  | 

1 Answer 1

Sorted by: Reset to default 0

I've had similar issues with converting to PDBs from AF3 cif files. Regardless, you can try using PyMol or ChimeraX. The former has python libraries, so you can batch convert if you have a lot of files. I'm unsure if this will be any better than OpenBabel though - I suspect there is information missing from the cif to make some of the other file types.

本文标签： bioinformaticsHow do you convert a cif file to a mol fileStack Overflow