Jmol/Storymorph: Difference between revisions

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== Anchors ==

In preparation for a morph, you assign each domain an anchor. If the anchor selection is within the domain, the center of mass of the anchor will move on a linear path from initial to final state. Atoms within the domain but far away from the anchor will move on curved paths if the rigid-body transformation from initial to final state involves a rotation, not just a translation. If the anchor selection is part of another domain, the morph algorithm will ensure that the distance of the domain to the anchor remains constant throughout the morph. In essence, the other domain "drags along" the domain in question. To maintain connectivity between domains linke by a single covalent bond, an appropriate anchor would be the atom or residue the domain is directly attached to. If their are multiple covelent connections between domains, you can choose the anchor to include all the connection points.

In preparation for a morph, you assign each domain an anchor. If the anchor selection is within the domain, the center of mass of the anchor will move on a linear path from initial to final state. Atoms within the domain but far away from the anchor will move on curved paths if the rigid-body transformation from initial to final state involves a rotation, not just a translation.

[[Image:Morph one cm.gif‎]] [[Image:Morph one anchor.gif‎]]

In the left example, the center of mass travels on a line. As a result, the base of the "P", which has the same position in the initial and final state, moves away from this position during the morph. In the right example, the base of the "P" was chosen as anchor. Now it travels on a straight line (or in this case stays put) while the other parts of the "P" travel on curved paths.

If the anchor selection is part of another domain, the morph algorithm will ensure that the distance of the domain to the anchor remains constant throughout the morph. In essence, the other domain "drags along" the domain in question. To maintain connectivity between domains linke by a single covalent bond, an appropriate anchor would be the atom or residue the domain is directly attached to. If their are multiple covelent connections between domains, you can choose the anchor to include all the connection points.

[[Image:Morph one cm.gif‎]] [[Image:Morph one anchor.gif‎]]

In the left example, both red and green objects have their respective centers of mass travel on a line. As a consequence, the connection between the objects, which is present in both the initial and final state, opens during the transition. In the right example, the anchor for the green object was chosen to be the base of the red "P". As a consequence, the green object travels on a more complicated path maintaining the connectivity.

== Loading the two structures ==

Jmol/Storymorph: Difference between revisions

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 == Anchors ==
-In preparation for a morph, you assign each domain an anchor. If the anchor selection is within the domain, the center of mass of the anchor will move on a linear path from initial to final state. Atoms within the domain but far away from the anchor will move on curved paths if the rigid-body transformation from initial to final state involves a rotation, not just a translation. If the anchor selection is part of another domain, the morph algorithm will ensure that the distance of the domain to the anchor remains constant throughout the morph. In essence, the other domain "drags along" the domain in question. To maintain connectivity between domains linke by a single covalent bond, an appropriate anchor would be the atom or residue the domain is directly attached to. If their are multiple covelent connections between domains, you can choose the anchor to include all the connection points.
+In preparation for a morph, you assign each domain an anchor. If the anchor selection is within the domain, the center of mass of the anchor will move on a linear path from initial to final state. Atoms within the domain but far away from the anchor will move on curved paths if the rigid-body transformation from initial to final state involves a rotation, not just a translation.
+[[Image:Morph one cm.gif‎]]  [[Image:Morph one anchor.gif‎]]
+In the left example, the center of mass travels on a line. As a result, the base of the "P", which has the same position in the initial and final state, moves away from this position during the morph. In the right example, the base of the "P" was chosen as anchor. Now it travels on a straight line (or in this case stays put) while the other parts of the "P" travel on curved paths.
+If the anchor selection is part of another domain, the morph algorithm will ensure that the distance of the domain to the anchor remains constant throughout the morph. In essence, the other domain "drags along" the domain in question. To maintain connectivity between domains linke by a single covalent bond, an appropriate anchor would be the atom or residue the domain is directly attached to. If their are multiple covelent connections between domains, you can choose the anchor to include all the connection points.
+[[Image:Morph one cm.gif‎]]  [[Image:Morph one anchor.gif‎]]
+In the left example, both red and green objects have their respective centers of mass travel on a line. As a consequence, the connection between the objects, which is present in both the initial and final state, opens during the transition. In the right example, the anchor for the green object was chosen to be the base of the red "P". As a consequence, the green object travels on a more complicated path maintaining the connectivity.
 == Loading the two structures ==