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RosettaCommons / PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
https://rosettacommons.github.io/PyRosetta.notebooks/
MIT License
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How can I convert protein torsional angles back to cartesian coordinates #89

Closed TianmingQu closed 1 year ago

TianmingQu commented 1 year ago

Dear Pyrosetta developers,

I am recently trying to do an analysis on protein dihedral angles.

I have all the dihedral angle atom information (their atom type, atom name, atom coordinates, and index from PDB) saved in a dictionary and I am able to calculate each dihedral angle (not only backbone ones, also improper ones) using packages like MDAnalysis.

Then I am adding a small change to each of the dihedral angles to see how this will influence the conformation of the original protein structure, which requires me to convert the modified dihedral angles back to cartesian coordinates, is there any way in Pyrosetta I can do this?

Thanks for any suggestions!

Best, Tianming

ajasja commented 1 year ago

I'm not sure this is the best place to ask -- I thought github was more for code related questions, code improvements and new features. It's probably best to ask on Slack or in the forums. What do you think @roccomoretti ? PS: Pyrosetta can definitely do this, have a look at the set phi/psi methods https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.05-Protein-Geometry.ipynb#Protein-Geometry

roccomoretti commented 1 year ago

Strictly speaking, the issues in this Github repository should be used for reporting issues about the notebooks in the repository. It's not intended as a general PyRosetta support venue. For general PyRosetta questions, the better place to ask is https://www.rosettacommons.org/forum