User:Wayne Decatur/Generate Unfolded Structures
From Proteopedia
This describes how to unfold whole or parts of chains in solved structures using Pymol. This maintains the covalent bonds.
This came up because 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.
Please note that while maintaining covalent bonds, this process will generate a distorted structure that is just for representational purposes and is not thermodynamically stable. To translate or rotate a chain or parts relative the rest of the structure see my page on moving parts or components of structures using Pymol.
To enable yourself to 'drag' the chain however you want:
- Toggle in the bottom right corner the text next to 'Selecting' until 'Residues' comes up.
- put the mouse into 3-button editing mode either using 'Mouse' menu in upper console or toggle it by clicking text next to 'Mouse mode'.
- Click on Auto-Sculpting in the Sculpting menu that is under the Build menu.
- Use control-left-click-and-drag to move the chain where you want it to go and it will move towards your mouse like it is trying to catch up but is in viscous solution.
- When things are where you want for that part of the chain, quickly click 'Deactivate' under the Sculpting menu. The chain will freeze where it is.
Add information on breaking disulfides first and reforming others. You may wish to break the disulfides to unfold the protein more than you could obtain if you did not:
- Either pick the two atoms (pk1 and pk1, they will be called in the list to the side in Pymol) by going into 3 button Editing mode and selecting the bond between the two atoms and hitting Ctrl-right-click or choose atom #1 (pk1) first by hitting Ctrl-middle-click as you touch the atom and then selecting the next (pk2) and doing the same.
- Once the two atoms are chosen, break the bond by entering 'unbond pk1,pk2' in the command line area in Pymol.
- 1gxv is a good structure to with which to try this.
Pages with supporting information:
- Modeling and Editing Structures Page at Pymol Wiki
- Posting about using Sculpting in Pymol to manipulate structures
- Has information on molecular sculpting with a fuller summary of what it is meant to be
Add link to bottom part of my Morphing page because might want to let Morphing server generate structures transitioning between the folded and modified states for making an animation.
