The relative sizes of atoms and bonds can be set relative to MµCalc's own internally-defined 'scale' parameter. By default this is a simple function of the unit cell dimensions a, b and c, but some unit cells, for example those elongated along one side or those containing many atoms, may not work well. You may also wish to standardise this between a series of diagrams.

The scale is a length in metres. Choose wisely!

Atoms can be coloured by element (in which case they follow the rather beautiful and intuitive jmol colour scheme) or by charge (in which case they are coloured differing degrees of red or blue for positive and negative, respectively, normalised by the largest charge value present). These colours can be overridden by…

The default appearance of atoms can be overridden with the custom atoms settings.

• The customisation is applied by element with an optional numerical identifier afterwards. In the absence of the index, all atoms of that element are affected, whereas adding it only affects those atoms which share that index.
• You can first choose whether the atom is visible at all: if not, the remaining options are not needed!
• The colour can be left as default, which means it will be defined by whichever colour scheme was chosen (see above), or can be specified as three comma-separated numbers between 0 and 255, representing the levels of red, green and blue present. Thus, 255,0,0 would be bright red, 0,255,0 would be bright green and 255,255,0 would be bright yellow. Further examples of colours' RGB values can be seen on the jmol colours page.
• The size can be chosen relative to the scale parameter, or in absolute units.
• The opacity of the atom can be adjusted between 0 and 1, where 0 is perfectly transparent (and thus rather pointless—just make it invisible!) and 1 is fully opaque (the default).

The magnetic moments are arrows drawn in proportion to the size of the moment on the atom. They can be shown or hidden.

The boundary of the first unit cell can optionally be shown as a white wireframe.

Whilst using the visualisation menu, the contents of the visual window are fairly frequently refreshed to reflect modifications made to the display settings. When dealing with large numbers of atoms or especially bonds, this can become annoying. It is therefore possible to disable these automatic redraws. Doing so makes another menu option appear to trigger a manual refresh.

It is possible to draw any number of structural unit cells along a crystal direction. This option allows use of the crystallographic unit cell, the magnetic unit cell, or a custom number along each crystal axes.

The magnetic field can be displayed as a set of arrows whose direction indicates that of the field, and whose colour indicates its magnitude. Choosing this option opens a sub-menu allowing adjustment of various options.

• A field filename needs to be chosen. The appropriate extension will be added automatically.
• Ranges over which the field will be displayed need to be chosen. These are given as a comma-separated list containing an even number of values, and specified in MHz at which a muon would precess in that field (ie the field in tesla multiplied by the muon gyromagnetic ratio. For example, if you had identified a single precession frequency at 3 MHz in your data, you might be interested in oscillations in the range 2–4 MHz, and would enter 2,4. Finding a second frequency at 6 MHz might lead you to try 2,4,5,7.
• You can have any colour bar as long as it's rainbow… It is scaled automatically to your range. Thus green, the central colour, might indicate the frequency you're looking for.

Bonds can be drawn between atoms as desired. They are drawn by MµCalc searching through pairs of visible atoms and drawing bonds between those specified. The bonds' appearance is also customisable.

• The 'from' element with option numerical index specifies the type of atom from which the bonds will start.
• The 'to' element specifies where they will end. It's fine if this is the same as the 'from' element.
• Setting a maximum length ensures that the entire unit cell doesn't become a haystack of criss-crossing bonds, and only adjacent-ish atoms are linked.
• It is also possible to specify a colour and radius, in much the same way as the size and colour of atoms is set (see above).

Your visualisation settings can be committed to an filetypes#json for use later or at a different computer.