Jmol/Useful one-liners
From Proteopedia
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<StructureSection load='' size='340' side='right' caption='' scene='86/865284/Myoglobin/1'> | <StructureSection load='' size='340' side='right' caption='' scene='86/865284/Myoglobin/1'> | ||
| + | ===Enhancing visibility=== | ||
set zshade on | set zshade on | ||
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<jmol><jmolButton><text>change hover text</text><script>hover "%n%R_%a"; font hover 30</script></jmolButton></jmol> | <jmol><jmolButton><text>change hover text</text><script>hover "%n%R_%a"; font hover 30</script></jmolButton></jmol> | ||
When spinning is off and you hover over an atom, you get some information. This one-liner increases the font size and condenses the information displayed, showing the one-letter residue name, the residue number and the atom name. | When spinning is off and you hover over an atom, you get some information. This one-liner increases the font size and condenses the information displayed, showing the one-letter residue name, the residue number and the atom name. | ||
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| - | color bonds green | ||
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| - | <jmol><jmolButton><text>color aromatic sidechains green</text><script>select aromatic and sidechain; color bonds green</script></jmolButton></jmol> | ||
| - | This colors the bonds of the selected atoms, but not the atoms themselves. This is useful to keep the atoms in CPK color scheme (showing which elements we have) while highlighting certain residues or side chains. | ||
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| - | center visible | ||
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| - | <jmol><jmolButton><text>center visible</text><script>center visible</script></jmolButton></jmol> | ||
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| - | This centers on all atoms that are visible, either explicitly or as part of a cartoon etc. | ||
set fontScaling ON | set fontScaling ON | ||
All labels created after this will scale as you zoom in or out of the structure. | All labels created after this will scale as you zoom in or out of the structure. | ||
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| - | model 0 | ||
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| - | When multiple models are loaded (e.g. NMR structures), or multiple structures are loaded (e.g. superpositions), this shows all the structures at the same time. | ||
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 button removes all representations of alternate conformations. | 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 button removes all representations of alternate conformations. | ||
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| + | ===Color bonds independently from atoms=== | ||
| + | color bonds green | ||
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| + | <jmol><jmolButton><text>color aromatic sidechains green</text><script>select aromatic and sidechain; color bonds green</script></jmolButton></jmol> | ||
| + | This colors the bonds of the selected atoms, but not the atoms themselves. This is useful to keep the atoms in CPK color scheme (showing which elements we have) while highlighting certain residues or side chains. | ||
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<jmol><jmolButton><text>hide %B</text><script>hide hidden or *%B</script></jmolButton></jmol> | <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> | <jmol><jmolButton><text>display %B</text><script>hide hidden and not *%B</script></jmolButton></jmol> | ||
| + | ===Saving selections and views for later use=== | ||
define aoi selected | define aoi selected | ||
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script inline @view1 | script inline @view1 | ||
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| + | ===Not yet categorized=== | ||
| + | center visible | ||
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| + | <jmol><jmolButton><text>center visible</text><script>center visible</script></jmolButton></jmol> | ||
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| + | This centers on all atoms that are visible, either explicitly or as part of a cartoon etc. | ||
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| + | model 0 | ||
| + | |||
| + | When multiple models are loaded (e.g. NMR structures), or multiple structures are loaded (e.g. superpositions), this shows all the structures at the same time. | ||
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</StructureSection> | </StructureSection> | ||
Revision as of 12:24, 28 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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