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Author: Vikram K. Mulligan (

Documentation created 24 April 2018.

Purpose and Description

The PolarGroupBurialPyMolStringMetric SimpleMetric was created to complement the buried_unsatisfied_penalty scoreterm. It generates a string of PyMol commands to colour the polar groups in a pose based on burial. The pose is coloured grey, with surface-exposed polar groups in cyan and buried groups in orange. The generated commands are written out with output PDB files.

The PolarGroupBurialPyMolStringMetric takes a scorefunction as input, and matches its definition of "burial" to that used by the buried_unsatisfied_penalty scoreterm. See the documentation for that scoreterm for the scorefunction options that can be altered to change the definition of burial.


<PolarGroupBurialPyMolStringMetric name="(&string)" verbose="(false &bool)" scorefxn="(&string)" />
  • verbose: If true, PyMol commands are also written to the tracer. False by default.
  • scorefxn: A previously-defined scorefunction, used to set the definition of "burial". See the documentation for the buried_unsatisfied_penalty scoreterm for settings that can be altered in the scorefunction to change the definition of burial. Required input.

See Also