DINO: Visualizing Structural Biology |
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User Manual
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A surface topograph is a 2-dimensional grid that contains a scalar height value at each grid-point. In contrast to the scalar field, which would require 4 dimensions to fully visualize it (see above), the surface topograph can be completely visualized in 3 dimensions by constructing a 3-dimensional surface from the grid and the height-values.
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Two topography object types are implemented:
A new object is created with the command new :
Syntax: .topo new [-name NAME] [-type TYPE] [-set SET] [-sel SEL]
If no name is given, the dataset-name is used. TYPE defaults to surface . SET can be a list with PVs (Table 18 (P. 42)) and SEL can include all selecteable element properties (see Table 19 (P. 43)).
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Following are all topography dataset commands:
new : create a new object (see "9.2 Topography Objects" on page 42)
set get : retrieve or modify a dataset property (Table 18 (P. 42))
Syntax: .topo set PV[, PV ...] .topo get P
restrict : shadow out a subset of the dataset which will not be considered in selection or property setting (see "5.1.7 Dataset Restriction" on page 25)
Syntax: .topo restrict SELECTION
delete : remove one or more objects
Syntax: .topo delete obj [obj2 ...]
attach : will attach topograph to a structure dataset (not yet implemented)
grab reset fix center : transformation related commands (see "5.1.8 Transformation" on page 25)
Commands directed against a topography object are issued as
Syntax: .topo.obj command [parameters]
Following is a list of all topography object commands:
renew : Similar to new command, except the type and name are already determined, so only selection and setting is possible. If either selection or setting (or both) are omitted, the current selection resp. setting is maintained.
Syntax: .topo.obj renew [-selection SEL] [-set SET]
show hide : turns display of the object in the graphics window on or off. Identical to clicking on the object name in the object menu (see see "4.12 The GUI" on page 20)
Syntax: .topo.obj show .topo.obj hide
set get : modify or retrieve topo object properties (See Table 18 (P. 42) and see "5.1.5 Modifying Objects" on page 23).
Syntax: .topo.obj get P .topo.obj set PV [-selection SEL] [-range [src=SRC][,PROP=prop][val=VAL1:VAL2]]
render : modifies the graphical appearance of an object (see "9.5 Render & Graphical Appearance" on page 44).
The command render modifies the graphical appearance of a topograph object:
Syntax: .topo.obj render PV [,PV ...]
Several rendering modes are available, specified as:
Syntax: .topo.obj render MODE
lighting is only applied to the front face, leaving the backside practically unlit and dark |
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Following is an example using a 6-fold symmetrized correlation average of an AFM-topograph of an HPI layer7:
// load a topography dataset load hpi.tiff // set scaling (in nm) .hpi set scalexy=33,scalez=3 // create a new object (of default type surface) .hpi new -name s // create a new contour object .hpi new -name c -type contour -set lstep=0.1 // color contour lines .hpi.c set color=yellow // color surface with range .hpi.s set color=red4:yellow -range prop=h,val=0:1