image [origin] [center] [triclinic | familiar [com <commask>]] [<mask>] [ bymol | byres | byatom ] [xoffset <x>] [yoffset <y>] [zoffset <z>]
[origin] Image to coordinate origin (0.0, 0.0, 0.0); default is to image to box center.
[center] For bymol/byres, image by center of mass; default is to image by first atom position.
[triclinic] Force imaging with triclinic code. This is the default for non-orthorhombic cells.
[familiar [com <commask>]] Image to truncated octahedron shape. If ’com <commask>’ is given, image with respect to the center of mass of atoms in <commask>.
[<mask>] Image atoms/residues/molecules in mask.
[bymol] Image by molecule (default).
[byres] Image by residue.
[byatom] Image by atom.
[xoffset <x>] Shift atoms by a factor of <x> in the X-direction.
[yoffset <y>] Shift atoms by a factor of <y> in the Y-direction.
[zoffset <z>] Shift atoms by a factor of <z> in the Z-direction.
Note this command is intended for advanced use; for most cases the autoimage command should be sufficient.
For periodic systems only, image molecules/residues/atoms that are outside of the box back into the box. Currently both orthorhombic and non-orthorhombic boxes are supported. A typical use of image is to move molecules back into the box after performing center. For example, the following commands move all atoms so that the center of residue 1 is at the center of the box, then image so that all molecules that are outside the box
after centering are wrapped back inside:
center :1 image
The xoffset etc. keywords can be used to shift the entire unit cell in a certain direction by the given factor, which can be useful for visualizing trajectories with periodic boundary conditions. For example, to generate a trajectory that is offset by 1.0 box length in the X direction, one could use:
image xoffset 1.0 trajout traj.offsetx1.nc