Jmol/Useful one-liners
From Proteopedia
(Difference between revisions)
(→Examples) |
(→Examples) |
||
| Line 23: | Line 23: | ||
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=== | ||
| Line 29: | Line 34: | ||
<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. | ||
| - | |||
| - | |||
| - | <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> | ||
===Saving selections and views for later use=== | ===Saving selections and views for later use=== | ||
Revision as of 12:25, 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.
Examples
| |||||||||||
