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Tool: Density Map Toolbar

The Density Map Toolbar provides a series of icons for changing the display of volume models (such as density maps) with a single click. Like other tools, this interface can be opened from the Tools menu (more...). See also: Graphics Toolbar, Molecule Display Toolbar, Mouse Modes for Right Button toolbar, making images

Clicking an icon shows the executed command in the Log. The selMaps specifier indicates the currently selected volume model(s), or if none are selected, all displayed volume models. Note there may be alternative commands for performing the same action.

Density Maps icon description command equivalent
show map volume selMaps show
hide map volume selMaps hide
isosurface volume selMaps style surface
mesh isosurface volume selMaps style mesh
map as image
(solid display)
volume selMaps style solid
step 1
(not subsampled, every point)
volume selMaps step 1
step 2
(subsampled at every other point)
volume selMaps step 2
fit map in map fitmap #N inMap #M

(fitting the lower-model-number of two maps total or selected into the other)

difference map volume subtract #N #M minRms

(subtracting the higher-model-number of two maps total or selected from the other)

smooth by Gaussian filtering volume gaussian #N sDev 6

(where N is the model number of a single selected map)

toggle transparency of surface or mesh (none, but see the transparency option of volume; applies to selMaps)
toggle outline box (none, but see the showOutlineBox option of volume; applies to selMaps)
single Z-plane at the center of the current region volume selMaps planes z orthoplanes off style solid
orthoplanes (exact volume command depends on the data, but sets orthoplanes at the center of the full data, with style solid region all)
full region volume selMaps region all orthoplanes off
2D projection (XYZ)
(affects solid display only)
volume selMaps projectionMode 2d-xyz
3D projection
(affects solid display only)
volume selMaps projectionMode 3d
Airways II preset
(affects solid display only)
volume selMaps appearance "Airways II"
CT_Skin preset
(affects solid display only)
volume selMaps appearance CT_Skin
initial threshold settings
(affects solid display only)
volume selMaps appearance initial

UCSF Resource for Biocomputing, Visualization, and Informatics / March 2019