Residue Pair Energy

[Anonymous]

Hi,

 

After protein interface design some of the residues are showing a significant difference In relative residue energy (difference between control and design in REU) . Therefore I wish to know about the residue pair energies and also the atom interaction that is contributing to the change in the total energy of the designed residue at the interface. I am using the following command line in pyrosetta after loading the PDB by the pose

 

pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies (50, pose, sfxn=’REF2015′, score_type=”total_score”, threshold=0.0)

 

pyrosetta.toolbox.atom_pair_energy.print_atom_pair_energy_table (sfxn=’ REF2015′, score_type=”total_score”, 50, 55, pose, threshold=0.0)

 

However it is not working. Kindly let me know if at all I am using the correct syntax and if there is another alternative for the same.

 

I am getting the following error

 

 

pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies (50, pose, sfxn=’REF2015′, score_type= ‘total_score’, threshold=0)

---

AttributeError                            Traceback (most recent call last)

<ipython-input-29-df17b5b63b20> in <module>()

—-> 1 pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies (50, pose, sfxn=’REF2015′, score_type= ‘total_score’, threshold=0)

/usr/local/lib/python2.7/dist-packages/pyrosetta-2017-py2.7-linux-x86_64.egg/pyrosetta/toolbox/atom_pair_energy.pyc in print_residue_pair_energies(res, pose, sfxn, score_type, threshold)

    212     “””

    213     for res_idx, score in _reisude_pair_energies(

–> 214         res, pose, sfxn, score_type, threshold

    215     ):

    216         print(“{0} {1}  {2}”.format(pose.residue(res_idx).name1(), res_idx, score))

/usr/local/lib/python2.7/dist-packages/pyrosetta-2017-py2.7-linux-x86_64.egg/pyrosetta/toolbox/atom_pair_energy.pyc in _reisude_pair_energies(res, pose, sfxn, score_type, threshold)

    170             residue i with the user-specified residue, res.

    171     “””

–> 172     sfxn.score(pose)

    173     for i in range(1, pose.total_residue() + 1):

    174         emap = rosetta.core.scoring.EMapVector()

AttributeError: ‘str’ object has no attribute ‘score’

Thanking you

 

 

 

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