Morphs: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis, Wayne Decatur, David Canner, Joel L. Sussman, Karsten Theis, Angel Herraez

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 ''Chemically possible'' (also sometimes called ''chemically plausible'', ''semi-plausible'', or ''chemically reasonable'') means that, at the least, correct covalent bond lengths and angles are maintained, and that atoms are constrained not to pass through each other. This type of morph requires sophisticated software, but luckily such software is freely available and easy to use.
+A minor disadvantage of energy-minimized morphs is that the movement in the animation may be rather jerky. In some cases the molecule resists the transition, so moves slowly at first, then rapidly and "uncomfortably" through the mid-point arriving quickly near the final configuration. In contrast, linear interpolation alone (see next section) produces a smooth animation which some people prefer.
 ====Yale Morph Server====
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 Another way to make "chemically reasonable" morphs is available from the [http://xray.bmc.uu.se/usf/mol_morph.html Biomolecular Morphing] site by Gerard J. Kleywegt at Uppsala University, Sweden. Unlike the Yale server, this is not a server where you can submit a job and get back finished results automatically. Kleywegt's LSQMAN software is downloadable for use on linux, and is free for academic and non-profit use.
-A minor disadvantage of energy-minimized morphs is that the movement in the animation may be rather jerky. In some cases the molecule resists the transition, so moves slowly at first, then rapidly and "uncomfortably" through the mid-point arriving quickly near the final configuration. In contrast, linear interpolation alone (see next section) produces a smooth animation which some people prefer.
 ===Linear Interpolation===