File specification of binary part of silent file (especially PDB section)

[Anonymous]

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 

[Anonymous]

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).

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