Jmol/Useful one-liners
From Proteopedia
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select selected and not *%B | select selected and not *%B | ||
| - | Deselects alternate conformations. Some models contain two conformations (labeled A and B in column 17 of a PDB file, with fractional occupancies adding up to 1, see e.g. [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/dealing-with-coordinates]. The example | + | Deselects alternate conformations. Some models contain two conformations (labeled A and B in column 17 of a PDB file, with fractional occupancies adding up to 1, see e.g. [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/dealing-with-coordinates]. The example buttons hide or show all representations of alternate conformations. |
| + | <jmol><jmolButton><text>hide %B</text><script>hide hidden or *%B</script></jmolButton></jmol> | ||
| + | <jmol><jmolButton><text>display %B</text><script>hide hidden and not *%B</script></jmolButton></jmol> | ||
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set zshade on | set zshade on | ||
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<jmol><jmolButton><text>3</text><script>set zshadepower 3</script></jmolButton></jmol> | <jmol><jmolButton><text>3</text><script>set zshadepower 3</script></jmolButton></jmol> | ||
<jmol><jmolButton><text>4</text><script>set zshadepower 4</script></jmolButton></jmol> | <jmol><jmolButton><text>4</text><script>set zshadepower 4</script></jmolButton></jmol> | ||
| - | This controls how | + | This controls how strongly the scene fades with distance. |
| - | <jmol><jmolButton><text>hide %B</text><script>hide hidden or *%B</script></jmolButton></jmol> | ||
| - | <jmol><jmolButton><text>display %B</text><script>hide hidden and not *%B</script></jmolButton></jmol> | ||
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===Color bonds independently from atoms=== | ===Color bonds independently from atoms=== | ||
Revision as of 13:17, 29 October 2020
This is a collection of useful one-liners in Jmol. While the Scene authoring tools give you access to a lot of Jmol's functionality, they don't cover the entire scripting language. However, the SAT contains an input box for entering Jmol commands directly. This page collects commands that might be entered into that textbox to achieve effects not otherwise possible. Viewers of Proteopedia pages might find occasional use of these one-liners as well. To enter them, you first have to right-click on the Jmol window and open a console. For more complex Jmol commands, see Jmol/Using the console.
Examples
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