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° | Link<Atom|Res|Mol|Obj|All> | - |
Find bonds automatically |
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| | | Command | | Argument | | Datatype | | Default | | Min | | Max | |
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| Format: | | Link<Atom|Res|Mol|Obj|All> | Selection, | |
SELECTION | | - | | - |
| - | | |
| | Deviation = Maximum allowed bond length deviation in % | | FLOAT | | 25.0 | | - | | - |
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| Python: | | Link<Atom|Res|Mol|Obj|All>(selection1,deviation=None) |
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| Menu: | | Edit > Find links | |
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| Related: | | AddBond , DelBond | | ||||||||||
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| Required: | |  |
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The Link
command measures the distances between all atoms in the selection and adds a bond
whenever two atoms are close enough. 'Close enough' means that their distance is smaller than the sum of their bond radii multiplied with
100% plus the allowed deviation:
| (1) |
The bond orders of the newly added bonds are also assigned automatically
.
As interactions with metal ions are treated purely electrostatically during molecular dynamics simulations,
they should not be selected with Link
to avoid the accidental assignment of covalent bonds.
Link assigns a maximum of four covalent bonds per atom.
Example 1:
LinkRes Man
Link all atoms in residues named 'Man' that are close enough to form a bond.
Example 2:
LinkMol C,Deviation=50%
Link all atoms in molecule 'C' that are close in space, even those that are
50% further apart than the sum of their bond radii.