Jmol/Storymorph: Difference between revisions
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[[Image:Spike labeled spacefill small.gif|right|border]] | [[Image:Spike labeled spacefill small.gif|right|border]] | ||
This is the documentation for Storymorph, a suite of Jmol functions to help with superimposing and morphing between two structures representing different conformations of a molecule or molecular assembly ([ | This is the documentation for Storymorph, a suite of Jmol functions to help with superimposing and morphing between two structures representing different conformations of a molecule or molecular assembly ([https://proteopedia.org/wiki/index.php/Image:Storymorph.spt script]). For more general information, see [[Jmol/superposition]] and [[Morphs]]. If you load storymorph.spt into a Jmol session where no structures have loaded or all structures have been removed using the "zap" command, it will run a demonstration superposition and morph based on calmodulin strutures. Most examples in this documentation are from this demo. | ||
== Overview of capabilities == | == Overview of capabilities == | ||
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# To focus on the N-terminal domain, superimpose Nterm, and run the "C anchored to N" morph. With this superposition, you can see the (less subtle) changes in the N-terminal domain, while the changes in the C-terminal domain are hardly perceptible. To explore how the anchoring helps to maintain covalent bonds, run the "independent domains" morph instead. To emphasize the distance of the link between the two domains (in this case, the distance between consecutive alpha carbon atoms), choose the "combo" representation and run the two morphs again (see animated GIF on the right. | # To focus on the N-terminal domain, superimpose Nterm, and run the "C anchored to N" morph. With this superposition, you can see the (less subtle) changes in the N-terminal domain, while the changes in the C-terminal domain are hardly perceptible. To explore how the anchoring helps to maintain covalent bonds, run the "independent domains" morph instead. To emphasize the distance of the link between the two domains (in this case, the distance between consecutive alpha carbon atoms), choose the "combo" representation and run the two morphs again (see animated GIF on the right. | ||
# To see a bad linear morph, superimpose "Nterm", check "skip rigid" and run any of the morphs. The reason the morph is bad is the large rotation of the C-terminal domain, foreshortening distances (e.g. "flattening" helices) in the middle of the trajectory in the absence of a rigid body movement. | # To see a bad linear morph, superimpose "Nterm", check "skip rigid" and run any of the morphs. The reason the morph is bad is the large rotation of the C-terminal domain, foreshortening distances (e.g. "flattening" helices) in the middle of the trajectory in the absence of a rigid body movement. | ||
# To see a good linear morph, superimpose "all", check "skip rigid" and run any of the morphs. Because the necessary rotations are | # To see a good linear morph, superimpose "all", check "skip rigid" and run any of the morphs. Because the necessary rotations are smaller in this case, the distortion of the domains is much smaller and hardly noticable as the domains are moving. | ||
== Two-phase Morph: rigid body followed by linear interpolation == | == Two-phase Morph: rigid body followed by linear interpolation == | ||
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<nowiki>structures = [{1.1}, {2.1}]</nowiki> | <nowiki>structures = [{1.1}, {2.1}]</nowiki> | ||
Here, the selection is the first and the second structure loaded. For models in a single-structure file, you would use "1.1" and "1.2" instead. For subunits with different conformation, you would select by chain name, e.g. | Here, the selection is the first and the second structure loaded. For models in a single-structure file, you would use "1.1" and "1.2" instead. For subunits with different conformation, you would select by chain name, e.g. chain="A" and chain="B". More complicated cases are possible (chain B of the second model vs. chain A of the third model) but probably rare. | ||
== Defining the domains == | == Defining the domains == | ||
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[[Lipase lid morph]] | [[Lipase lid morph]] | ||
[[Mfd translocase]] | |||
[[T7 RNA Polymerase]] | [[T7 RNA Polymerase]] | ||
