DINO: Visualizing Structural Biology
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9 Topography Dataset

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.

Topography Dataset and Object Properties

Property

S1

G2

Description

Dataset Properties

center

 

X

geometric center of dataset

scalexy

X

X

scaling factor of xy plane, default is 1.0

scalez

X

X

scaling factor of z-height, default is 1.0

trans

X

X

translation vector

rot

X

X

rotation matrix

Object Properties

center

 

X

geometric center of object

step

X

X

step-size along grid during object creation

lstart

X

X

relativ contour level start, value between 0.0 and 1.0

lend

X

X

relativ contour level end, value between 0.0 and 1.0

lstep

X

X

relativ contour level step, value between 0.0 and 1.0

9.1 Attachments

Attachments are not yet implemented for the topography dataset.

9.2 Topography Objects

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)).

Topography Dataset Element Properties

property

S3

G4

L5

R6

Description

color

X

 

 

 

color of element

u

 

 

X

X

u-value of original topograph

v

 

 

X

X

v-value of original topograph

h

 

 

X

X

height

9.3 Topography Dataset Commands

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)

9.4 Topography Object Commands

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).

9.5 Render & Graphical Appearance

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

where MODE is one of:

9.6 Example

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

1. indicates that this property can be modified with set

2. indicates that this property can be retrieved with get

3. property can be modified with set

4. property can be retrieved with set

5. selecteable property

6. property can be used in range statement

7. D.J. Muller, D. Fotiadis, A. Engel FEBS Letters 430 (1998)