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Bug with make_pose_from_sequence when incorporating non-standard ResidueTypes in PyRosetta

I've been trying to assemble a poly-peptoid sequence using the make_pose_from_sequence function, however there seems to be an error in the way the polymer gets connected in the pose. For instance, the command:

make_pose_from_sequence(pose, "AAX[P02]AA", "fa_standard")

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Residue_energy_breakdown utility

I am planning to analyze residue interactions using residue_energy_breakdown utility as written in the documentation. However I could not find "residue_energy_breakdown" command in rosetta_source/bin.

I've built Rosetta3.3 in RedHat 5.4 by "scons bin mode=release" and build seemed to be finished without any problem.
Should I do any other things to use residue_energy_breakdown?

Thank you,

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docking in rosetta 3.3

i am new to rosetta. I have installed rosetta 3.3 in ubuntu linux 10.10. I wanted to do protein-protein docking & protein-peptide docking. so, can u help me to do this things. i have read the manuals of rosetta3.3 but i m unable to understand it correctly.Can you show me some direction to do this things & also how to create input files .pdb with only atom details for docking n other things also.............

thank you.....................

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Surface accessible residue as a constraint.


I wonder if anyone has any ideas how I might do this. I have a protein where I know some of the surface exposed residues (from labelling experiments) and I was wondering if there was a way to use this as a constraint in structure production. For example is it possible to say that the amines (Nz) of lysines X,Y and Z must be solvent exposed?

Thanks for any suggestions you might have.

Best wishes


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