Lac repressor morph methods: Difference between revisions
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===Linear Interpolation=== | ===Linear Interpolation=== | ||
The [[Morphs|interpolation for the morph]] is linear. No corrections were done to make interatomic distances or angles be chemically realistic. Because Jmol assigns covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious "bonds" appear and then disappear in some regions of the interpolated frames during wireframe animations of the morph. These appear as "wads" of bonds or "cobwebs". | The [[Morphs|interpolation for the morph]] is linear. No corrections were done to make interatomic distances or angles be [[Morphs|chemically realistic]. Because Jmol assigns covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious "bonds" appear and then disappear in some regions of the interpolated frames during wireframe animations of the morph. These appear as "wads" of bonds or "cobwebs". | ||
The interpolation was done with the [http://www.umass.edu/microbio/rasmol/pdbtools.htm freely available DOS program morph2.exe], inserting 10 (or in some cases 12) frames between the two empirical end points (after all hydrogens were removed with DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabytes. For the morph showing specific contacts as hydrogen bonds, 8 carefully selected hydrogen atoms were re-inserted into the start and end models prior to doing the interpolation. | The interpolation was done with the [http://www.umass.edu/microbio/rasmol/pdbtools.htm freely available DOS program morph2.exe], inserting 10 (or in some cases 12) frames between the two empirical end points (after all hydrogens were removed with DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabytes. For the morph showing specific contacts as hydrogen bonds, 8 carefully selected hydrogen atoms were re-inserted into the start and end models prior to doing the interpolation. | ||
