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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. Map icons act on the currently selected volume models, if any (specified as sel), otherwise the currently displayed volume models (specified as a list of model numbers). There may be alternative commands for performing the same action.

Density Maps icon description command
show map volume show
hide map volume hide
isosurface volume style surface
mesh isosurface volume style mesh
image display volume style image
toggle transparency of surface or mesh
(if a mix of transparent and opaque surfaces, change all to opaque)
volume with the transparency option
toggle outline box volume with the showOutlineBox option
step 1
(not subsampled, every point)
volume step 1
step 2
(subsampled at every other point)
volume step 2
single Z-plane at the center of the current region volume 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 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 projectionMode 2d-xyz
3D projection
(affects image display only)
volume projectionMode 3d
Airways II preset
(affects image display only)
volume appearance "Airways II"
CT_Skin preset
(affects image display only)
volume appearance CT_Skin
initial threshold settings
(affects image display only)
volume appearance initial

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