User:Wayne Decatur/Generate Unfolded Structures: Difference between revisions
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<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td valign='top'>[[Image:Note.gif|left]] '''Theoretical Structure Will Result:''' | <table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td valign='top'>[[Image:Note.gif|left]] '''Theoretical Structure Will Result:''' | ||
The protein structure that will result from manipulations suggested on this page will be [[theoretical models|theoretical]], and hence should be interpreted with caution.</td></tr></table> | The protein structure that will result from manipulations suggested on this page will be [[theoretical models|theoretical]], and hence should be interpreted with caution.</td></tr></table> | ||
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 | 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. | ||
===2024 automated or scripted way=== | |||
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. | 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... | ||
===Older way with Auto-Sculpting in PyMOL=== | |||
This came up because [https://people.chem.umass.edu/cbobst/Members.html Adriana Zeledon] wanted to generate structures derived from her structure of interest where parts were unfolded or folded differently. I thought this could very useful for illustrative or conceptualizing purposes for many users. For maybe simulating denaturing, conformational changes, or other dynamic processes. | This came up because [https://people.chem.umass.edu/cbobst/Members.html Adriana Zeledon] wanted to generate structures derived from her structure of interest where parts were unfolded or folded differently. I thought this could very useful for illustrative or conceptualizing purposes for many users. For maybe simulating denaturing, conformational changes, or other dynamic processes. | ||
