pyrosetta workhops help: notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb

[ascusf]

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Can I ask these questions here?

I am currently working on the PyRosetta workshops and had a few questions regarding the notebook titled "Membrane Protein ∆∆G of Mutation" (notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb) available in the PyRosetta GitHub repository: https://github.com/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb

I encountered an error when using the 3gp6.pdb file that I downloaded. As an alternative, I downloaded the 1mm4.pdb file mentioned in the research paper. However, the REU values obtained from 1mm4.pdb were unusually high. Eventually, I found the 3gp6_A.pdb file located at notebooks/inputs/3gp6_A.pdb, which yielded faster and consistent results. Could you please explain how the 3gp6_A.pdb file was prepared to better correlate with the data?

Regarding the cutoff of 1.5 REU, I obtained the same graph but I could not Identify the amino acids. Did you calculate it as PREDICTED_VALUES - EXPERIMENTAL_VALUES?
[image]

Did you convert the REU to kcal/mol?
Thank you for your assistance!

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