User:Wayne Decatur/Moving Components or Parts of Structures
From Proteopedia
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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 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 here and press the 'launch binder' badge (or alternatively 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
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 Modeling and Editing Structures page at the Pymol Wiki.
Manually:
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 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.
Under the 'Mouse' menu in the top console window, select 'three button editing' (or toggle this by clicking the words next to 'Mouse mode' in the bottom left corner.
At the bottom left corner of the viewer, toggle selecting 'Objects' or 'Molecules' by clicking the text next to 'Selecting' to toggle the correct choice.
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 "drag coordinates" from action menu for object and then holding down shify worked and then had to rotate using command 'rotate x,90, obj05'.
This is covered on the 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.
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 Modeling and Editing Structures page or by selecting the interested section (using sequence bar [sequence under 'display' menu] 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.
If you want to move parts of chains relative the rest no longer maintaining the original structural constraints, see my page on using Pymol to generate unfolded structures.
Supporting pages:
- Modeling and Editing Structures page
- Page with info on editing structures
- Has some other information on moving elements relative others
- Intro page with some help
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.
