CCP4 Molecular Graphics Documentation
	View Menu

Opens the window



The bottom line of this window is a molecule selection widget which you can use to select a chain, residue or atom. By default, when you click Find or Find&close the display will recentre on the selected atom(s) and will label them. If the Centre on selected atom(s) button is toggled off then the atom(s) will only be labelled. By default the orientation of the view is not changed but if Rotate camera to view in direction of CA-HA bond is toggled on then, if the selected residue is an amino acid, the orientation will be changed as specified. This interface can also be used to select residues around the specified atoms: toggle on the Select residues within.. button and set the radius as required. If the for all models button is on then a sphere of atoms will be selected for all of the models. Note that the selection is applied to the first display object for each model; these selection options are probably most useful if there is one display object per model.

Preferences for the tools on this menu can be found in the Preferences window (on the Tools pull-down menu), in the Display folder click View menu preferences.

Stereo can be toggled on/off. The stereo mode can be selected in the Preferences. The stereo angle can be set; the default value (for CCP4mg 1.1) of -6 degrees gives wall-eye stereo or a positive value gives cross-eye stereo.
Show axes Show the axes in top right corner of display window
Depth queue fog Fogging distant objects creates the illusion of depth. The fog density is graded between the front and back clipping planes and the density can be altered by opening the Clip plane/depth cue slider described below. Also the default of applying fogging to text labels can be switched off in the Preferences window.
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. It can also be controlled by..
Clip plane/depth cue slider If toggled on a panel is opened at the bottom of the main graphics window with sliders controlling the clip plane separation and fog thickness.
Background colour can be selected from the defined colours.
Lighting style See lighting.
Set transparency A window like this is shown:



All of the display objects are listed and initially have opacity set to 1.0 in a range of 0.0-1.0 (i.e. they are totally opaque) - setting this to 0.1-0.4 will make objects transparent. Transparency is not applied until the Transparency on/off button at the top of the window is toggled on. Note that drawing transparent objects is slow and proportional to the total displayed and not just the size of the transparent object.
Compact display table Toggling this on will remove the display objects from the display table so only the data objects are listed. Clicking on the data object line in the table will toggle the listing of its display objects.
View from Reorients the display to view from left,right,top,bottom or back.

Save view or Restore view to file, similar to saving the program status.
Align view on click this button after selecting a plane from the menu.
Sliders to set specific translation, rotation and zoom. Click the Apply button to apply.