Jmol/Useful one-liners: Difference between revisions
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This expands the selection to include all atoms belonging to the same residues or groups than the currently selected atoms. [This command is available in the SAT in a perhaps unexpected spot: in the selections tab, in the select within distance box, the second button]. | This expands the selection to include all atoms belonging to the same residues or groups than the currently selected atoms. [This command is available in the SAT in a perhaps unexpected spot: in the selections tab, in the select within distance box, the second button]. | ||
===Showing backbone torsion angles phi and psi | ===Showing backbone torsion angles phi and psi=== | ||
ramachandran selected | ramachandran selected | ||
<scene name='77/778341/Phi_psi/1'> | <scene name='77/778341/Phi_psi/1'>phi and psi in an alpha helix</scene> | ||
===Not yet categorized=== | ===Not yet categorized=== | ||
center visible | center visible | ||
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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. | 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. | ||
Synonyms: <code>model 0, frame all, frame 0</code> | Synonyms: <code>model 0, frame all, frame 0</code> | ||
zoom 0 | |||
Zoom out so that all displayed atoms etc. fit into the window (also centers on visible) | |||
<jmol><jmolButton><text>zoom visible</text><script>zoom 0</script></jmolButton></jmol> | |||
set perspectiveDepth ON | |||
Perspective depth shows close objects larger than those far away. Orthoscopic view shows them at the same size. When looking at crystal symmetry, orthoscopic is sometimes preferable. Try it for <scene name='82/824000/Contacts/4'>cellulose structure</scene>. | |||
<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>set perspectiveDepth ON</scriptWhenChecked> | |||
<scriptWhenUnchecked>set perspectiveDepth OFF</scriptWhenUnchecked> | |||
<checked>true</checked> | |||
<text>Perspective depth</text> | |||
</jmolCheckbox> | |||
</jmol> | |||
moveto quaternion (61 and mainchain) | |||
Orients residue 61 in a specific way. If you use the same command on another amino acid residue, the C-alpha atom and its bonds will be oriented in the same way. This makes it easier to compare side chain conformations. | |||
</StructureSection> | </StructureSection> | ||
