Revise Atom, Basic Tab
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Dialog Box - called from: Input Atoms Dialog

See the Temperature Factor Tab for modification or entry of temperature factors, the Central Distance and Slice Offset tabs for adjusting boundaries for individual atoms, and the Vector Tab for atomic vectors for magnetic moments or vibrational displacements.

Label. Each atom may be assigned a label of up to 6 characters. Labels in ATOMS may not contain any embedded blanks. Any embedded blanks or leading blanks in labels will be converted to underscores. Trailing blanks will be stripped. These labels may now contain non-ANSI characters - see Character Sets. A superscript in roman numerals giving the symmetry operation which generates each atom may optionally be appended to the label on the drawing - this is selected in the Atom Labels dialog (Display menu).

Fractional coordinates. For crystals, the x, y and z coordinates should be in fractions of the unit cell. However, if you are drawing a molecule and have chosen unit Cartesian reference axes, the coordinates should be in Angstroms.

Irrational coordinates. In some hexagonal and trigonal space groups there are special positions with coordinates like 2/3, 1/3, 1/6 etc. Such irrational coordinates should be entered to at least the fifth decimal place - for example 0.66667 instead of 0.67 or 0.667. ATOMS must apply finite tolerance in the generation of all atomic positions, and the second form is not precise enough - multiple atoms will be generated instead of one atom on the special position.

Type. The atom type is used when locating bonds and polyhedra; it is usually expedient to enter the same type for all atoms which are bonded similarly (e.g. all carbons, all silicons, all six-coordinated cations, all oxygens, etc.) to save effort in defining bonds and polyhedra. The atomic number can usually be used for the type, although there are situations in which different type numbers should be used for the same element (see Polyhedra). For diffraction calculations (Powder, Precession) the type number must be the atomic number, or a number which gives an entry to the scattering factor table, modulo 100. That is, type numbers 6, 106, 206, 306 etc. will be read as atomic number 6 (carbon). Thus it is recommended that whenever possible type numbers be the atomic number, with added 100's if necessary to differentiate bonds and polyhedra.

Radius. Each atom will be represented by a sphere of this radius, unless it is involved in a polyhedron defined in the polyhedra input. If an atom is given radius 0.0, it will never be plotted as a sphere and will only appear (as a corner) if it is involved as ligand in a complete coordination polyhedron. Bonds to such atoms will not be plotted unless the atoms are ligands in polyhedra. Thus if you want to show only polyhedra and never the individual atoms, give radii of 0.0 to all the atoms which may be involved, either as central atoms or as ligands. Even if you use positive radii for the atoms, you can switch off display of the atoms in incomplete polyhedra with a checkbox in the Polyhedra dialog (Input1 menu). However, using a radius of 0.0 omits calculation of bonds to atoms in incomplete polyhedra, which can improve computation time and conserve memory.

If you do not want to show an atom at all, but want to show the bonds to the atom, that is draw a wire-frame model, enter a negative number for the radius. The absolute value of the radius can still be used in the Generate Bonds from Atomic Radii option. If atoms with negative radii are involved in polyhedra, they will be treated in the same way as atoms with positive radii.

For ball-and-stick drawings of typical structures, radii of about half the ionic or covalent radii usually work well. For space-filling or interpenetration the covalent radii can be multiplied by a number larger than one. All radii can be changed simultaneously by a given factor with the Atoms - Global dialog in the Input1 menu.

Colors and patterns/shades. Each atom always has a rim and a fill, the colors for which are specified independently. Rims are turned on and off, and their widths are set, in the Line Widths dialog in the Input2 menu. Shading applies only to fills. See Input Colors/Patterns/Pens for general aspects of input.

If you have checked the Use individual atom distances box in the boundary option Enter Forms, or the Use individual atom offsets box in the boundary option Slice, you should use the Set Boundary Forms button (Central Distances for Individual Atom or Slice Offsets for Individual Atom dialogs) to correct the central distance or offset for each form, up to six forms for distances. These distances or offsets are the ones which are actually used for the boundaries, but the central distances or offsets entered for each form in the boundary option are used for display of crystal shape and to set up the initial search intervals, so the individual distances or offsets should not be too different.

Shubnikov. This checkbox determines whether the equivalents of this particular input atom show vectors or other Shubnikov indicators (+ or -). Set the orientation of atomic vectors in the Vector Tab, and set the overall properties of vectors in the Vector dialog, called from the Input1 menu or the Input Atoms dialog.

Protein. This only applies to structure input from Protein Data Bank files. It calls up a dialog (Protein) which gives protein specific information about the atom.

Line Width. If the Use individual box for atoms in the Line Widths dialog (Input2 menu) is checked, the width specified here will be used, rather than the overall value in the Line Widths dialog.

Hachure patterns are macroscopic patterns of lines which may be drawn within the outlines of atoms. These are useful for black-and-white output in situations where shading patterns are not reproduced very well, or a more definite pattern differentiation is desirable. The patterns are simply drawn in 2 dimensions and do not vary with attitude of the surface like the hachure patterns for Polyhedra.

Hachure patterns are not used in the 3D Drawing Modes, and this entire section is not applicable to 3D display/output.

The Spacing is the distance between lines, in Angstroms. The colors/shades of the patterns are same as those selected for the outlines or edges (above), and the widths are also as selected (above) for each individual atom type, or as selected overall in the Line Widths dialog (Input2 menu).

If the Use shade box is checked, the gray shade selected in this dialog will also be applied as fill, in addition to the pattern, in black-and-white non-shaded output. This choice overrides the Use initial patterns box in the Shading dialog (Input2 menu). Shading, as selected in the Shading dialog (Input2 menu) is applied independently of hachure patterns, and it is possible to have both, either in color or black and white. In color display and output, the fill color (above) is always used.