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' a chain in a structure however you want: | ===To enable yourself to 'drag' a chain in a structure however you want:=== | ||
* Load the structure into Pymol with all the consoles open. | * 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. | ||
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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. | 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. | ||
Breaking disulfide bonds with Pymol: | ===Breaking disulfide bonds with Pymol:=== | ||
* 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. | * 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. | * 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. | * [[1gxv]] is a good structure to with which to try this. | ||
If you want to form new disulfide bonds after you modified the structure: | ===If you want to form new disulfide bonds after you modified the structure:=== | ||
* Use the 'bond' command to link the gamma sulfur atoms of the resides of interest. For example, if we were joining resiues 37 and 82, 'bond 37/sg,82/sg' | * Use the 'bond' command to link the gamma sulfur atoms of the resides of interest. For example, if we were joining resiues 37 and 82, 'bond 37/sg,82/sg' | ||
* Then enter the command 'unpick' to hide the 'bond baton' that gets displayed. | * Then enter the command 'unpick' to hide the 'bond baton' that gets displayed. | ||
===Morphing=== | |||
To make clear the changes that took place to get to the modified structure, you may want to submit the original and modified structures to the [http://www.molmovdb.org/cgi-bin/beta.cgi Yale Morph Server] and let it generate the steps needed to go from one structure to the other and make an animation with this collection of structures. | |||
Pages with supporting information | ==Pages with supporting information== | ||
*[http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures Page at Pymol Wiki] | *[http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures Page at Pymol Wiki] | ||
*[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg01890.html Posting about using Sculpting in Pymol to manipulate structures] | *[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg01890.html Posting about using Sculpting in Pymol to manipulate structures] | ||
*[http://www.rubor.de/bioinf/tips_advanced.html Has information on molecular sculpting with a fuller summary of what it is meant to be] | *[http://www.rubor.de/bioinf/tips_advanced.html Has information on molecular sculpting with a fuller summary of what it is meant to be] | ||
* [http://pymol.sourceforge.net/newman/user/S0260cartoons.html Pymol Users manual page on secondary structure] | * [http://pymol.sourceforge.net/newman/user/S0260cartoons.html Pymol Users manual page on secondary structure] | ||