Jmol/Storymorph: Difference between revisions
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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 == | ||
