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=== | ||
