Jmol/Using the console
From Proteopedia
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===Surfaces=== | ===Surfaces=== | ||
| + | The "isosurface" command in Jmol draws all kind of surfaces (molecular surface, electron density, orbitals) with all kinds of coloring options (by atom, electrostatic potential, conservation, distance, etc.). It is a complex command, so examples help to learn how to use it. | ||
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| + | <scene name='86/862210/Ammonia/2'>Ammonia with lone pair cartoon</scene> | ||
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| + | <scene name='86/864093/Water/1'>electrostatic potential of water</scene> | ||
===Electron density=== | ===Electron density=== | ||
| + | The way electron density is usually shown is as surface, but it warrants its own category because getting the electron density data is a special topic (also discussed at [[User:Karsten Theis/Electron density]]. | ||
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===Superpositions=== | ===Superpositions=== | ||
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Because bonds of side chains and modifications are drawn in a single command, the covalent links between them will also be drawn. | Because bonds of side chains and modifications are drawn in a single command, the covalent links between them will also be drawn. | ||
| - | Here is an example, <scene name='78/786673/Gal_overal_view/ | + | Here is an example, <scene name='78/786673/Gal_overal_view/2'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used]. |
<jmol><jmolButton><text>zoom in</text><script>moveto 1.0 { 752 -659 33 153.48} 738.33 0.0 0.0 {-32.029 70.295 112.187} 53.8932808874789 {0 0 0} 0 0 0 3.0 0.0 0.0;</script></jmolButton></jmol> | <jmol><jmolButton><text>zoom in</text><script>moveto 1.0 { 752 -659 33 153.48} 738.33 0.0 0.0 {-32.029 70.295 112.187} 53.8932808874789 {0 0 0} 0 0 0 3.0 0.0 0.0;</script></jmolButton></jmol> | ||
</StructureSection> | </StructureSection> | ||
Current revision
The Jmol console may be used to obtain information, and to change the scene currently displayed. This may be useful while viewing a Proteopedia page, or while creating a 3D scene, achieving certain effects not possible with the Scene Authoring Tools alone. You can open the Jmol console via the right-click menu in the Jmol window, or via a dedicated button under the Jmol window in the SAT.
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