Jmol/Useful one-liners: Difference between revisions
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<jmol><jmolButton><text>save orientation view1</text><script>save orientation view1</script></jmolButton></jmol> | <jmol><jmolButton><text>save orientation view1</text><script>save orientation view1</script></jmolButton></jmol> | ||
<jmol><jmolButton><text>restore orientation view1</text><script>restore orientation view1</script></jmolButton></jmol> | <jmol><jmolButton><text>restore orientation view1</text><script>restore orientation view1</script></jmolButton></jmol> | ||
===Contacts=== | |||
contact (selected)(not selected) | |||
This shows all contacts between the selected atoms and the remainder of the structure, using colored disks to show the contacts and their distances. If you want to exclude covalent bonds, do this | |||
contact (selected)(not selected and not within(1.8, selected)) | |||
Here is an example of the <scene name='82/824000/Contacts/4'>contacts of one glucose unit</scene> in a cellulose model. This used the additional parameter "full" to show pillows (of intersection vanderWaals spheres) instead of disks. | |||
===Expanding selection to whole residue/groups=== | ===Expanding selection to whole residue/groups=== | ||
select within(group, selected) | select within(group, selected) | ||
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]. | ||
