Jmol/Useful one-liners: Difference between revisions
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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. | ||
<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> | |||
===Color bonds independently from atoms=== | ===Color bonds independently from atoms=== | ||
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<jmol><jmolButton><text>color aromatic sidechains green</text><script>select aromatic and sidechain; color bonds green</script></jmolButton></jmol> | <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. | 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. | ||
===Saving selections and views for later use=== | ===Saving selections and views for later use=== | ||
Revision as of 15:25, 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.
ExamplesExamples
Enhancing visibilityset zshade on
This fades the scene (to white if the background is white, to black if the background is black) for atoms further away from the viewer, giving a better 3D feel even when the model is not moving. hover "%n%R %a"; font hover 30
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. set fontScaling ON All labels created after this will scale as you zoom in or out of the structure. 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. [1]. The example button removes all representations of alternate conformations.
Color bonds independently from atomscolor bonds green
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. Saving selections and views for later usedefine aoi selected Defines the currently selected atoms as "aoi". You can use this later in commands such as "select aoi" to select the atoms again. view1 = script("show moveto")
Saves the current orientation in the variable "view1". Later, you can go back to this view using: script inline @view1 Not yet categorizedcenter visible
This centers on all atoms that are visible, either explicitly or as part of a cartoon etc. 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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