Hi there,
I would like to know if somebody could share the binary file format specification of the silent file. I try to read the PDB section without any luck. Before digging through the code of extract_pdb I thought it would be faster to quickly ask how to read the binary section.
Thank you very much.
Cheers,
Max
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There is no written specification, it's just serialized C++ objects. I think each line is one Residue object but I'm not sure. The only program that can read/write the format is Rosetta itself - generally one "extracts" interesting models from the binary silent file to PDB for further use. There is an executable for the purpose (extract_pdbs or similar).
Efforts have been made to make the system robust against code changes, but broadly only the version of rosetta that wrote a binary silent file can reliably extract from it. (It also needs to be on similar machine architecture).