User:Wayne Decatur/Moving Components or Parts of Structures - Revision history

Wayne Decatur: /* 2024 automated or scripted way to unfold a segment of a protein chain */

2024-03-07T21:47:36Z

2024 automated or scripted way to unfold a segment of a protein chain

← Older revision		Revision as of 21:47, 7 March 2024
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	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>

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

	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.


			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.

	===Adjusting by hand===		===Adjusting by hand===

Wayne Decatur: fix heading

2024-03-05T22:09:48Z

fix heading

← Older revision		Revision as of 22:09, 5 March 2024
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	====Adjusting by hand===		===Adjusting by hand===

	This describes how to do this in Pymol and assumes you initiate a session with the console containing the menubar.		This describes how to do this in Pymol and assumes you initiate a session with the console containing the menubar.

Wayne Decatur: reference new stuff

2024-03-05T22:09:30Z

reference new stuff

← Older revision		Revision as of 22:09, 5 March 2024
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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 do this in Pymol and assumes you ~~initate~~ a session with the console containing the menubar.
			===2024 automated or scripted way to unfold a segment of a protein chain===

			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.




			====Adjusting by hand===

			This describes how to do this in Pymol and assumes you initiate a session with the console containing the menubar.

	Using Pymol commands to do this via commands is described at the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] at the Pymol Wiki.		Using Pymol commands to do this via commands is described at the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] at the Pymol Wiki.

Wayne Decatur at 21:10, 19 June 2014

2014-06-19T21:10:17Z

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	This describes how to do this in Pymol and assumes you initate a session with the console containing the menubar.		This describes how to do this in Pymol and assumes you initate a session with the console containing the menubar.

	Using Pymol commands to do this in commands is described at the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] at the Pymol Wiki.		Using Pymol commands to do this via commands is described at the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] at the Pymol Wiki.

	Manually:		Manually:

Wayne Decatur at 15:20, 5 August 2011

2011-08-05T15:20:27Z

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	Now activate the object you want and while hold down 'SHIFT', click left-button, middle-button, or right-button and drag to rotate, move in x and y plane or to move in z plane, respectively.		Now activate the object you want and while hold down 'SHIFT', click left-button, middle-button, or right-button and drag to rotate, move in x and y plane or to move in z plane, respectively.

			''Note: On a Mac, I didn't find it that easy to do as described above (for example, cannot seem to toggle selection of objects using toggle or even selection under mouse) and instead had to activate <nowiki>"drag coordinates"</nowiki> from action menu for object and then holding down shify worked and then had to rotate using command <nowiki>'rotate x,90, obj05'</nowiki>.''

	This is covered on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] under 'Manual superposition of two molecules' near the bottom of the page; however it assumes there are already two objects.		This is covered on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] under 'Manual superposition of two molecules' near the bottom of the page; however it assumes there are already two objects.

Wayne Decatur at 02:21, 19 December 2010

2010-12-19T02:21:28Z

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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 do this in Pymol and assumes you initate a session with the console containing the menubar.		This describes how to do this in Pymol and assumes you initate a session with the console containing the menubar.

Wayne Decatur at 06:55, 8 January 2010

2010-01-08T06:55:40Z

← Older revision		Revision as of 06:55, 8 January 2010
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	To translate and/or rotate a separate chain (or object you made) within a solved structure relative other chains (or objects):		To translate and/or rotate a separate chain (or object you made) within a solved structure relative other chains (or objects):
	Make the chain you want to move a separate object by .~~.... FILL IN~~		Make the chain you want to move a separate object by selecting (for example, entering 'select chain d' on command line) and then using action menu next to that selection ('sele') for that selection to 'extract object'.

	Lock objects to remain in place using 'action' on side menu and selecting 'movement' and 'protect' for each.		Lock objects to remain in place using 'action' on side menu and selecting 'movement' and 'protect' for each.
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	To translate and/or rotate part of a chain in a structure relative the rest without:		To translate and/or rotate part of a chain in a structure relative the rest without:
	Select part to move and split it off from the original structure either using commands as outlined on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] or by selecting the interested section (using sequence bar or selection commands) and making it a separate object????? VERIFY THIS AND EASIEST WAY TO NOT HAVE THAT PART DUPLICATED.???		Select part to move and split it off from the original structure either using commands as outlined on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] or by selecting the interested section (using sequence bar <nowiki>[</nowiki>sequence under 'display' menu<nowiki>]</nowiki> or selection commands) and making it a separate object????? VERIFY THIS AND EASIEST WAY TO NOT HAVE THAT PART DUPLICATED.???

	Now you essentially do as in the first part to translate and/or rotate this object relative the other structural components. However, while the moving part won't simply be a separate chain, but a separate object to Pymol, most commands and actions are the same.		Now you essentially do as in the first part to translate and/or rotate this object relative the other structural components. However, while the moving part won't simply be a separate chain, but a separate object to Pymol, most commands and actions are the same.

Wayne Decatur at 23:12, 20 May 2009

2009-05-20T23:12:47Z

← Older revision		Revision as of 23:12, 20 May 2009
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	This describes how to do this in Pymol and assumes you initate a session with the console containing the menubar.		This describes how to do this in Pymol and assumes you initate a session with the console containing the menubar.

	Using Pymol commands to do this in commands is described at the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] at the Pymol Wiki.		Using Pymol commands to do this in commands is described at the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] at the Pymol Wiki.
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	Select part to move and split it off from the original structure either using commands as outlined on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] or by selecting the interested section (using sequence bar or selection commands) and making it a separate object????? VERIFY THIS AND EASIEST WAY TO NOT HAVE THAT PART DUPLICATED.???		Select part to move and split it off from the original structure either using commands as outlined on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] or by selecting the interested section (using sequence bar or selection commands) and making it a separate object????? VERIFY THIS AND EASIEST WAY TO NOT HAVE THAT PART DUPLICATED.???

	Now you essentially do as in the first part to translate and/or rotate this object relative the other structural components. However, while the moving part won't simply be a separate chain, but a ~~seperate~~ object to Pymol, most commands and actions are the same.		Now you essentially do as in the first part to translate and/or rotate this object relative the other structural components. However, while the moving part won't simply be a separate chain, but a separate object to Pymol, most commands and actions are the same.


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	*[http://www.rubor.de/bioinf/tips_advanced.html Has some other information on moving elements relative others] <br>		*[http://www.rubor.de/bioinf/tips_advanced.html Has some other information on moving elements relative others] <br>
	*[http://www.cem.msu.edu/~posey/cem181h/PyMOLtutorial05/tutorial05.htm Intro page with some help] <br>		*[http://www.cem.msu.edu/~posey/cem181h/PyMOLtutorial05/tutorial05.htm Intro page with some help] <br>

			Similar manipulations can be done with separate structures in SWISS-PDB viewer by toggling off movement in the layers control panel for the layer to remain in place.

Wayne Decatur at 22:25, 20 May 2009

2009-05-20T22:25:31Z

← Older revision		Revision as of 22:25, 20 May 2009
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	To translate and/or rotate a separate chain (or object you made) within a solved structure relative other chains (or objects):		To translate and/or rotate a separate chain (or object you made) within a solved structure relative other chains (or objects):
	Make the chain you want to move a ~~seperate~~ object by.....		Make the chain you want to move a separate object by ..... FILL IN

	Lock objects to remain in place using 'action' on side menu and selecting 'movement' and 'protect' for each.		Lock objects to remain in place using 'action' on side menu and selecting 'movement' and 'protect' for each.
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	Now activate the object you want and while hold down 'SHIFT', click left-button, middle-button, or right-button and drag to rotate, move in x and y plane or to move in z plane, respectively.		Now activate the object you want and while hold down 'SHIFT', click left-button, middle-button, or right-button and drag to rotate, move in x and y plane or to move in z plane, respectively.

			This is covered on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page] under 'Manual superposition of two molecules' near the bottom of the page; however it assumes there are already two objects.

Wayne Decatur at 22:17, 20 May 2009

2009-05-20T22:17:05Z

← Older revision		Revision as of 22:17, 20 May 2009
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	*[http://www.ccp4.ac.uk/newsletters/newsletter40/11_pymol.html Page with info on editing structures] <br>		*[http://www.ccp4.ac.uk/newsletters/newsletter40/11_pymol.html Page with info on editing structures] <br>
	*[http://www.rubor.de/bioinf/tips_advanced.html Has some other information on moving elements relative others] <br>		*[http://www.rubor.de/bioinf/tips_advanced.html Has some other information on moving elements relative others] <br>
	[http://www.cem.msu.edu/~posey/cem181h/PyMOLtutorial05/tutorial05.htm Intro page with some help] <br>		*[http://www.cem.msu.edu/~posey/cem181h/PyMOLtutorial05/tutorial05.htm Intro page with some help] <br>