SciViz Software tools

Overview Tutorials to Get Started with Molecular Visualization and High-end 3D animation
Molecular Flipbook (coming soon)
Molecular Dynamics introduction movie

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: 

  1. Open PyMOL
  2. Type fetch 3ql3
  3. Type fetch 4m6k
  4. Click the Zoom button at the top right to see everything in your scene
  5. In the menu on the right, click the A button next to [4m6k]
  6. Drag down/left to select Action:align>AlignTo:molecule>Object:3ql3
  7. 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
  8. Color the molecules: Click the rainbow colored C button on the far right of [3ql3] and pick Color:Reds>Red
  9. Repeat for 4m6k to pick Cyan

Using selections:

  1. Restart PyMOL to ensure we are on the same page
  2. Type fetch 3vkh (Dynein dimer (motor protein that walks on microtubules composed of tubulin) with more complete stalk on one monomer)
  3. Type fetch 3j1t (short piece of the microtubule-binding stalk of dynein bound to a tubulin dimer
  4. Click the Zoom button at the top right to see everything in your scene
  5. 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.
  6. Try a default alignment: In the menu on the right, click the A button next to [3j1t]
  7. Drag down/left to select Action:align>AlignTo:molecule>Object:3vkh
  8. 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
  9. First make a selection, then align that selection as follows:
  10. Top menu click Display>Sequence On
  11. 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... 
  12. You will see a new object in your menu called (sele).  Rename this by clicking the A button and type "mtBinder"
  13. Next to [mtBinder] click A Align:AlignTo:molecule>Object:3vkh
  14. 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
  15. 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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Graham Johnson,
Dec 17, 2012, 3:45 PM
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