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It is recommended that the Clean PDB API be used to pre-process any PDB file which was not originally generated by Rosetta.

Running RosettaHoles

RosettaHoles can be run with the following command:

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• a PDB file with voids indicated as virtual Atoms

• the rosetta logs, which contain a variety of scoring information

Interpreting Output

The holes in the output PDB are indicated using virtual HETATM records at the end of the PDB file, all of which have the atom name V, the resid CAV and chain Z. The radius of each void in Å is stored in the b-factor column of the PDB file.

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