Jmol/Storymorph: Difference between revisions
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# To see the changes in the C-terminal domain, move model 2 to minimize distances between the two conformations of this domain (i.e. choose superimpose Cterm). Check the Palindrome box, and display model 1 only. Then, click the morph button labeled "N anchored to C". If you want to focus on the changes in the C-terminal domain, also select the consecutive timing option. | # To see the changes in the C-terminal domain, move model 2 to minimize distances between the two conformations of this domain (i.e. choose superimpose Cterm). Check the Palindrome box, and display model 1 only. Then, click the morph button labeled "N anchored to C". If you want to focus on the changes in the C-terminal domain, also select the consecutive timing option. | ||
# To focus on the N-terminal domain, superimpose Nterm, and run the "C anchored to N" morph. 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. | # To focus on the N-terminal domain, superimpose Nterm, and run the "C anchored to N" morph. 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. | ||
# 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. | # 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. | ||
# To see a good linear morph, superimpose all, check "skip rigid" and run any of the morphs. Because the necessary rotations are smeller 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 == | ||