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° | Pos<Atom|Res|Mol> |
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Set/get atom positions |
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| | | Command | | Argument | | Datatype | | Default | | Min | | Max | |
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| Format: | | Pos<Atom|Res|Mol> | Selection, | |
SELECTION | | - | | - |
| - | | |
| | X = X-Position in Å, | | FLOAT | | - | | - | | - | | |||
| | Y = Y-Position in Å, |
| FLOAT | | - | | - | | - |
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| | Z = Z-Position in Å, |
| FLOAT | | - | | - | | - |
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| | CoordSys = local | global, | | STRING | | local | | - | | - | | |||
| | Mean = Yes | No | | STRING | | No | | - | | - |
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| Python: | | Pos<Atom|Res|Mol>(selection1,x,y,z,coordsys,mean) resultlist = Pos<Atom|Res|Mol>(selection1) |
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| Menu: | | Effects > Position > Set/Get |
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| Related: | | Move |
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| Required: | |
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The PosAtom, PosRes
and PosMol commands set or get the position of one or more units in the specified coordinate system.
In the majority of cases, the coordinates of interest are those in the
local coordinate system of the object the atom belongs to,
i.e. those shown in the atom property HUD and
PDB files. If the CoordSys parameter
is set to 'global', then the atom coordinates refer to YASARA's global coordinate system
, where 0/0/0 is the window center, the Y-axis points upwards and the Z-axis points into the screen.
Results are normally returned per atom, unless the Mean parameter
is set to 'yes', in which case the geometric center of the selected atoms is returned.
Example 1:
PosAtom 500,X=-10,Y=20,Z=30
Place atom 500 at position -10/20/30 in the object's local coordinate system.
Example 2:
PosAtom 600,0,0,0,CoordSys=global
Place atom 600 at position 0/0/0 in the global coordinate system
(the center of the screen).
Example 3:
PosAtom Obj 1crn,Mean=Yes
Get the mean atom position in the local coordinate system of object
1crn, i.e. the geometric center.
Example 4:
PosAtom Obj 1crn,X=10,Y=8,Z=-3,Mean=Yes
Shift the atoms in object 1crn such that the mean position,
i.e. the geometric center, gets the coordinates 10/8/-3.
Example 5:
PosAtom CA
Get the local positions of all Calpha atoms.
Example 6:
PosAtom 100,CoordSys=global
Get the position of atom 100 in the global coordinate system
.
Example 7:
x,y,z = PosAtom 500
Assign the position of atom 500 in the object's local coordinate system
to variables 'x','y' and 'z'.
Example 8:
x,y,z = PosRes Lys 50
Assign the position of the geometric center of residue Lys
50 to variables 'x','y' and 'z'.
Example 9:
pos() = PosAtom 600,CoordSys=global
Assign the current position of atom 600 in the global coordinate system
to the list 'pos'.