Bond: Difference between revisions
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'''bond''' creates a new bond between two [[selection]]s, each of which should contain one atom. You can easily create a new bond by selecting two atoms, each with the CTRL-MIDDLE-MOUSE-BUTTON and typing "bond" on the command line. | |||
'''bond''' creates a new bond between two | |||
In order to visualize the newly created bond, [[lines]] or [[sticks]] have to be [[show]]n for both atoms. | |||
===USAGE=== | ===USAGE=== | ||
bond [atom1, atom2 [,order]] | bond [atom1, atom2 [,order]] | ||
atom1 and atom2 must either be selections (created by the [[select]] command, for example) or chosen using the PkAt mouse action (Ctrl+Middle mouse button). order is an optional integer (default is 1). | |||
Example usage: | |||
bond resi 1 and name NE2, resi 10 and name ND1 | |||
===PYMOL API=== | ===PYMOL API=== | ||
cmd.bond(string atom1, string atom2) | cmd.bond(string atom1, string atom2) | ||
where atom1 and atom2 are selections. | |||
===NOTES=== | ===NOTES=== | ||
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[[Category:Commands|Bond]] | [[Category:Commands|Bond]] | ||
[[Category:Editing Module|Bond]] | |||
Latest revision as of 07:43, 4 September 2024
bond creates a new bond between two selections, each of which should contain one atom. You can easily create a new bond by selecting two atoms, each with the CTRL-MIDDLE-MOUSE-BUTTON and typing "bond" on the command line.
In order to visualize the newly created bond, lines or sticks have to be shown for both atoms.
USAGE
bond [atom1, atom2 [,order]]
atom1 and atom2 must either be selections (created by the select command, for example) or chosen using the PkAt mouse action (Ctrl+Middle mouse button). order is an optional integer (default is 1).
Example usage:
bond resi 1 and name NE2, resi 10 and name ND1
PYMOL API
cmd.bond(string atom1, string atom2)
where atom1 and atom2 are selections.
NOTES
The atoms must both be within the same object.
The default behavior is to create a bond between the (lb) and (rb) selections.