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Toolbar: Map

Icons in the Map tab of the Toolbar act on volume models such as density maps. See also: 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. 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
image display volume selMaps style image
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)
step 1
(not subsampled, every point)
volume selMaps step 1
step 2
(subsampled at every other point)
volume selMaps step 2
single Z-plane at the center of the current region volume selMaps planes z orthoplanes off style image
orthoplanes (exact volume command depends on the data, but sets orthoplanes at the center of the full data, with style image region all)
full region volume selMaps region all orthoplanes off
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)

2D-XYZ projection
(affects image display only)
volume selMaps projectionMode 2d-xyz
3D projection
(affects image display only)
volume selMaps projectionMode 3d
Airways II preset
(affects image display only)
volume selMaps appearance "Airways II"
CT_Skin preset
(affects image display only)
volume selMaps appearance CT_Skin
initial threshold settings
(affects image display only)
volume selMaps appearance initial

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