User:Wayne Decatur/Generate Unfolded Structures: Difference between revisions
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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 [[User:Wayne Decatur/Moving Components or Parts of Structures| my page on moving parts or components of structures using Pymol]]. | 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 [[User:Wayne Decatur/Moving Components or Parts of Structures| my page on moving parts or components of structures using Pymol]]. | ||
To enable yourself to 'drag' | To enable yourself to 'drag' a chain in a structure however you want: | ||
* Load the structure into Pymol with all the consoles open. | |||
* Toggle in the bottom right corner the text next to 'Selecting' until 'Residues' comes up. | * 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'. | * 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'. | ||
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* Save your modified structure. | * Save your modified structure. | ||
You may wish to break the disulfides to unfold the protein more than you could obtain if you did not: | Disulfide bonds are covalent bonds that will remain maintained when you do the above process; however this may not be the behavior you wish for some or all of these bonds. You may wish to break the disulfides to unfold the protein more than you could obtain if you did not using the above process. | ||
* 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 | Breaking disulfide bonds with Pymol: | ||
*[[1gxv]] is a good structure to with which to try this. | * Either pick the two atoms (pk1 and pk1, they will be called in the list to the side in Pymol) in the bond 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. You will see '(pk1)' and '(pk2)' in the list to the right of the structure. | ||
* Once the two atoms are chosen, break the bond by entering 'unbond pk1,pk2' in a command line area in Pymol. | |||
* [[1gxv]] is a good structure to with which to try this. | |||
If you want to form new disulfide bonds after you modified the structure: | |||
