XBS file format

hofmann can read the .bs and .mv file formats from the original XBS ball-and-stick viewer by Methfessel (1995).

The .bs format

A .bs file defines atoms, species styles, and bond rules as a sequence of keyword lines. Blank lines and lines starting with * are comments.

atom

Defines an atom position:

atom  <species>  <x>  <y>  <z>

Example:

atom  C   0.000  0.000  0.000
atom  H   1.155  1.155  1.155

spec

Sets the display radius and colour for a species:

spec  <species>  <radius>  <colour>

Colour can be:

• A single float for grey (0.0 = black, 1.0 = white)

• Three floats for RGB (each in [0, 1])

• A CSS colour name

Example:

spec  C  1.000  0.7
spec  H  0.700  1.00
spec  O  0.900  1.0  0.0  0.0

bonds

Declares a bond detection rule between two species:

bonds  <sp1>  <sp2>  <min_len>  <max_len>  <radius>  <colour>

Bonds are detected between all atom pairs of the given species whose distance falls within [min_len, max_len].

Example:

bonds  C  H  0.000  3.400  0.109  1.00
bonds  H  H  0.000  2.800  0.109  1.00

poly

Declares a coordination polyhedron rule:

poly  <centre_sp>  [alpha]  [colour]

Polyhedra are drawn around atoms of species <centre_sp> using bonded neighbours as vertices. The optional alpha sets face transparency (default 0.4). Colour can be a grey float or three RGB floats; if omitted, the centre atom’s colour is used.

Example:

poly  Ti  0.3  0.5 0.7 1.0

Complete example (CH4)

atom      C       0.000      0.000      0.000
atom      H       1.155      1.155      1.155
atom      H      -1.155     -1.155      1.155
atom      H       1.155     -1.155     -1.155
atom      H      -1.155      1.155     -1.155

spec      C      1.000   0.7
spec      H      0.700   1.00

bonds     C     H    0.000    3.400    0.109   1.00
bonds     H     H    0.000    2.800    0.109   1.00

The .mv format

The .mv format stores multi-frame trajectories (e.g. from molecular dynamics). Each frame is introduced by a frame line, followed by coordinates for all atoms listed sequentially:

frame <label>
<x1> <y1> <z1> <x2> <y2> <z2> ...

Numbers may be split across lines. Lines starting with * and blank lines are comments.

Example:

frame step_0
0.0 0.0 0.0  1.155 1.155 1.155  -1.155 -1.155 1.155
1.155 -1.155 -1.155  -1.155 1.155 -1.155

frame step_1
0.01 0.0 0.0  1.16 1.16 1.16  -1.16 -1.16 1.16
1.16 -1.16 -1.16  -1.16 1.16 -1.16