User:Wayne Decatur/Generate Unfolded Structures: Difference between revisions
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This describes how to unfold whole or parts of chains in solved structures using Pymol. This maintains the covalent bonds. Also below is how to alter disulfide bonds in a structure using Pymol. | This describes how to unfold whole or parts of chains in solved structures using Pymol. This maintains the covalent bonds. Also below is how to alter disulfide bonds in a structure using Pymol. | ||
See [https://www.biostars.org/p/9588134/#9589058 my answer here to 'How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?'] for an option to do this in a scripted in PyMOL or automated way with PyMOL by setting dihedral angles for a span of amino acids to represent an unfolded state. Importantly, you can do with an PDB that has a protein chain by specifying the PDB id code and chain and region without needing to install anything on your system. | See [https://www.biostars.org/p/9588134/#9589058 my answer here to the question on Biostars entitled 'How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?'] for an option to do this in a scripted in PyMOL or automated way with PyMOL by setting dihedral angles for a span of amino acids to represent an unfolded state. Importantly, you can do with an PDB that has a protein chain by specifying the PDB id code and chain and region without needing to install anything on your system. | ||
Below is the older way of doing this with Auto-Sculpting in PyMOL... | Below is the older way of doing this with Auto-Sculpting in PyMOL... | ||
