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Edit menu
Display menu
Animate display

Edit menu

For all data
Hide Hide (i.e. make invisible) all data objects. The data object icon will be greyed out to indicate that the object is hidden.
Show Show (i.e. make visible) all data objects. The data object icon will be a coloured. Note that if some of the display objects are hidden (indicated by greyed-out icon) then they will remain hidden.
Close Close all of the data object. You will be asked to confirm.
For all display objects
Hide labels
Stop flashing
Undo transparency

Display menu

Display history
Undo and redo the display changes.
Clear picked labels
Clear all atom labels created by picking or Finding an atom. Note the Preferences option Picked atom labels in the Model display folder controls the behaviour of picked atom labels.
Toggle display of the toolbar. To customise the toolbar click on it with the right mouse button and choose Customise from the popup menu.
Depth queue fog
Toggle the depth queue fog. Fogging distant objects creates the illusion of depth. The fog density is graded between the front and back fog planes.
Clip front/back
Clip planes are two planes perpendicular to the z-direction (i.e. the planes are parallel to the screen); only objects between the front and back clipping plane are displayed. Limiting the display in the z-direction simplifies the picture when you are trying to focus on a small area. The clip plane separation is controlled by moving the cursor up-down with the h-key and th middle mouse button depressed.
Clip and fog details
Toggle the display of coordinate axes in the main window.
Background colour
Set the colour for the main graphics window background.
Solid smoothing
Animate display
A tool to set up flashing display objects. See below
See lighting.

Animate display

Two or more different display states can be saved. The program will continuously flash between these saved states whilst still allowing the user to control the view.

The Setup animation option opens a window similar to the Movie editor and Presentation window in which two or more states can be saved. The only difference in state that the program currently recognises is changes to visibility.

The animation can be toggled on or off from the Display pull-down menu or from the Action menu associated with the Setup animation window.

The Animation window has an Edit menu with a Preferences option which opens a window with options to set the time delay and to choose between cycling or oscillating through the snapshots.


Open the preferences window by selecting Preferences from the bottom of the Edit menu. The left panel of the window lists folders, click on the folder name to open the folder and click on the preference title to present the preferences on the right side of the window. Note that most preferences require you to hit the Apply button for changes to take effect.

All preferences are saved automatically to the program status file and so are saved and restored between sessions.

For some preferences Model display->Drawing style, Surfaces->Surface parameters the global preference can be over-ridden by setting preferences for individual display objects.

The groups of preferences are described below:

Model display
Model drawing style shows parameters for display objects such are spheres and ribbons. See examples.
HBonds/contacts drawing style shows parameters for display of HBonds and Contacts.
Atom label style By default when a model is loaded it is not labelled with atomIDs. The Put labels on option in these preferences can be set so models are automatically labelled. There is a list of atom properties which can be selected for inclusion in the label. The format of the atom label is the Coordinate ID. All model display objects have an Atom labels options on the icon menu which will override the options set here.
Picked atom label style There is a list of atom properties which can be selected for inclusion in the label of a picked atom. The format of the atom label is the Coordinate ID. To avoid cluttering the display the program will automatically limit the number of picked labels to Max picked labels by deleting the oldest labels. You can change the number of labels or set it to 999 (effectively no limit).
Model colours
The various colour schemes are defined. It is possible, for example, to reset the default colour for a carbon atom. It is possible to override colour scheme defined here by selecting Edit colour scheme.. from the Colour menu for each individually model display object.
For schemes where a colour is applied dependent of some floating point value (e.g. temperature factor) see Colouring by Atom/Residue Property.
Model analysis
Monomer types Specify the type of a monomer (e.g. 'amino_acid' or 'solvent') for use in the atom selection interface.
Hydrogen bonds Set the parameters for calculating hydrogen bonds.
Close contacts Set the parameters for calculating close contacts.
Secondary structure Set the parameters for calculating secondary structure.
Solvent accessible surface Parameters for colouring by solvent accessible surface area and buried area.
See Surfaces.
Surface drawing style See Surface drawing style preferences
Electrostatic surface colours See Electrostatic Potential Surfaces and Colouring by Atom/Residue Property.
Map drawing style See Map drawing style preferences
Render qualityThe Solid object render quality isSmooth by default. The drawing style is improved by drawing more and finer facets for each solid object surface so there is a trade-off between quality and speed and the appropriate setting will depend on the size of your computer versus the size of your models. When CCP4mg creates output images it automatically redraws with optimal quality - this is not affected by the render quality set here.
Fonts There are four different types of text in the program: atom labels, picked atom labels, annotation and legend. Each type can have a different default font; annotation and legend objects have a Font.. option on the icon menu to override the default. The font names listed in the interface are those fonts found on your system. Font names that begin with a capital letter are anti-aliased fonts which will usually be better quality but we have known them to be handled badly (no text is drawn) on some hardware.
Animation and fashing.See Animation section.
Images and Movies
See Images.
Screenshots See Screenshot preferences
Movie compile See Movie compile
Mouse bindings See Mouse bindings.
Session options
Restore status on restart This is on by default and the program status is restored to the last exit status. See Program Status.
Backup data files on exit By default off. If switched on then all currently used data files will be saved. See backing up data files.
Plugin preferences