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:'''

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 ~~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.

===2024 automated or scripted way to 'unfold' a range of residues in a protein structure===

I provide a Jupyter notebook file and an environment where it will actively work to let PyMOL do this is largely automated way after setting a few settings. The notebook will produce a modified PDB file with the specified span of amino acids adjusted to have phi, psi and omega angles representing an unfolded state. I'll come back to the specifics on how to get started doing that after mentioning where can find more details and a script for doing that in the standard PyMOL GUI-based software. For the details on that and a script you can edit and run with your favorite protein structure directly in PyMOL, 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?'].

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. It works for entries in the Protein Data Bank if you have the PDB id code and the chain designation. Go [https://github.com/fomightez/pymol-binder here] and press the '<code>launch binder</code>' badge (or alternatively [https://mybinder.org/v2/gh/fomightez/pymol-binder/master?filepath=index.ipynb just click here to launch]) and then when the Jupyter session comes up, choose from the available notebooks, 'Demo of Unfolding Region of Protein Chain via PyMOL'. Then step through running the notebook. I suggest step through first running it with the settings there to see how it works and then change the settings to what you want for the next run. It uses PyMOL headlessly in the session to do the adjustments of the torsional angles.

It should be adjustable with some hand editing to use custom, private/un-released PDB files uploaded to the session, too. (You can drag and drop from your local system into the file browser panel that appears in the left side of the JupyterLab interface in the session.)

Download the modified PDB file from the temporary session.

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.

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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:'''
 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 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.
+===2024 automated or scripted way to 'unfold' a range of residues in a protein structure===
+I provide a Jupyter notebook file and an environment where it will actively work to let PyMOL do this is largely automated way after setting a few settings. The notebook will produce a modified PDB file with the specified span of amino acids adjusted to have phi, psi and omega angles representing an unfolded state. I'll come back to the specifics on how to get started doing that after mentioning where can find more details and a script for doing that in the standard PyMOL GUI-based software.    For the details on that and a script you can edit and run with your favorite protein structure directly in PyMOL, 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?'].
+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. It works for entries in the Protein Data Bank if you have the PDB id code and the chain designation.  Go [https://github.com/fomightez/pymol-binder here] and press the '<code>launch binder</code>' badge (or alternatively [https://mybinder.org/v2/gh/fomightez/pymol-binder/master?filepath=index.ipynb just click here to launch]) and then when the Jupyter session comes up, choose from the available notebooks, 'Demo of Unfolding Region of Protein Chain via PyMOL'. Then step through running the notebook. I suggest step through first running it with the settings there to see how it works and then change the settings to what you want for the next run. It uses PyMOL headlessly in the session to do the adjustments of the torsional angles.
+It should be adjustable with some hand editing to use custom, private/un-released PDB files uploaded to the session, too.  (You can drag and drop from your local system into the file browser panel that appears in the left side of the JupyterLab interface in the session.)
+Download the modified PDB file from the temporary session.
 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.