Overview Tutorials to Get Started with Molecular Visualization and High-end 3D animation
Molecular Viewers Offering Animation Capabilities
Scientific Plugins for High-end 3D Animation Software Packages autoPACk/cellPACk
Web-servers to build or modify PDB files and other molecular files CORINA interactive 3D structure generator- build molecules interactively with nice/standard chemistry stick figure drawing and other types of inputs
Tutorials: Using PyMOL to align structures Basic:
- Open PyMOL
- Type fetch 3ql3
- Type fetch 4m6k
- Click the Zoom button at the top right to see everything in your scene
- In the menu on the right, click the A button next to [4m6k]
- Drag down/left to select Action:align>AlignTo:molecule>Object:3ql3
- The molecule 4m6k will snap onto the other one- its easier to see the relationship with ribbon cartoons, so in the top of the menu click the A button next to all and drag down/left to select Action:preset>publication
- Color the molecules: Click the rainbow colored C button on the far right of [3ql3] and pick Color:Reds>Red
- Repeat for 4m6k to pick Cyan
Using selections: - Restart PyMOL to ensure we are on the same page
- Type fetch 3vkh (Dynein dimer (motor protein that walks on microtubules composed of tubulin) with more complete stalk on one monomer)
- Type fetch 3j1t (short piece of the microtubule-binding stalk of dynein bound to a tubulin dimer
- Click the Zoom button at the top right to see everything in your scene
- Show both structures as cartoon ribbons colored by chain: In the menu on the right click the A button next to all and select Action:preset>publication, then click the rainbow colored C button on the right of the same row to select Color:byChain>byChain. You should end up with cyan, green, and magenta ribbon structures.
- Try a default alignment: In the menu on the right, click the A button next to [3j1t]
- Drag down/left to select Action:align>AlignTo:molecule>Object:3vkh
- This puts the 3j1t somewhere in the middle of the large motor domain of chain A of 3vkh- this is very bad! The problem is that PyMOL is trying to align the entire structure, including the tubulin of 3j1t to 3vkh- we only want to align the homologous part of the total structure
- First make a selection, then align that selection as follows:
- Top menu click Display>Sequence On
- In the bottom row, click the first K in chain A, which is residue 3264 of chain A, then scroll to the end of chain A in the sequence viewer to find the last residue of chain A which is also a K (last letter in green), hold shift and click to select all of chain A...
- You will see a new object in your menu called (sele). Rename this by clicking the A button and type "mtBinder"
- Next to [mtBinder] click A Align:AlignTo:molecule>Object:3vkh
- Now the stalk and the associated tubulin dimer of 3j1t (i.e. all of 3j1t) will properly align to the end of the stalk of chain A in 3vkh
- Click the A button next to [mtBinder] and select zoom, now you can rotate around and color the mtBinder red to get a good comparison of the fit of the microtubule binding regions from these two different structures.
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 Updating...
Ċ Graham Johnson, Dec 17, 2012, 3:45 PM
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