8 Scalar Field Dataset

The scalar field dataset is a 3-dimensional grid that contains a single scalar value at each grid point. To visualize it fully would require a 4-dimensional representation, which is currently beyond the capabilities of a computer workstation One interpretation is called iso-contouring, which creates an iso-surface from the scalar field with each point on the surface (ideally) having the same scalar value. Another interpretation is to draw each grid-point with its scalar value represented as a point of varying thickness, or to blend the grid points as a texture (as exploited in medical resonance imaging, also called volume rendering).

The grid is regular, but needs not be cubic. It can consist of arbitrary axis a, b and c with arbitrary angles α , β and γ . Its origin (grid point 0,0,0) will be mapped to some point in cartesian space (offset).

Probably the three most common uses for scalar fields in structural biology are electron density from x-ray data, 3D reconstructions from electron microscopy and electrostatic potential maps from theoretical calculations.

Scalar Field Dataset and Object Properties
Property	S1	G2	Description
Dataset Properties
center		X	geometric center of dataset
rot	X	X	rotation matrix, default is identity
trans	X	X	translation vector, default is identity
edge	X	X	value used beyond defined grid-point, default is 0.0
scale	X	X	scalar factor that is multiplied with every coordinate prior to object creation, existing objects must be renewed, default is 1.0
Object Properties
center	X	X	center of object, default is center of dataset
size	X	X	size of object in grid-units; can be either a scalar (cubic size) or in form of {xs,ys,zs}, default is 30
level	X	X	(object type contour) contour level, if s is appended then value is interpreted as sigma (standard deviation) units, default is 0.0
step	X	X	step-size along grid during object creation, default is 1
color	X		(object type contour) uniform color for object, default is white

8.1 Scalar Field Objects

A scalar field object is created with the command new . In contrast to the structure and surface dataset, the -set parameter is quite important, while the selection is not often employed.

Syntax: .scal new [-name NAME] [-type T][-selection SEL][-set SET]

NAME defaults to the name of the dataset. SET can be any of the settables object properties (see Table 15 (P. 38)). There are two scalar field object types:

contour : creates an iso-surface around center , with dimensions size , at the scalar value level , using a step-size of step . This is the default type.
grid : creates a grid around center , with dimensions size , using a step-size of step , the resulting points are displayed with radius radius

Example: .scal new -name m -set center=[.struct], size=40,level=1.5s, color=blue

         .scal new -name g -type grid -set size=40

Although a selection can already be given during object creation, its maybe easier to call a renew (to keep the lines short):

Example: .scal.m renew -sel 10<>.struct.inhib

All scalar field object properties except color will not take immediate effect, only when a renew (see below) is called. This is usually combined:

Example: .map new -name m -set center=[.map],size=40,level=1.0s
         // change the size
         .map.m renew -set size=50
         // change the level
         .map.m renew -set level=1.2s

Scalar Field Dataset Element Properties
property	S3	G4	L5	R6	Description
color	X				(for object type grid) color of individual grid point
radius	X				(for object type grid) radius of individual grid point
v			X	X	absolut value

8.2 Scalar Field Dataset Commands

Following are all scalar field dataset commands:

new : create a new object (see "8.1 Scalar Field Objects" on page 38).

set get : retrieve or modify a dataset property (Table 15 (P. 38)).

Syntax: .scal set PV[, PV ...] 
        .scal 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: .scal restrict SELECTION

delete : remove one or more objects.

Syntax: .scal delete obj [obj2 ...]

grab reset fix center : transformation related commands (see "5.1.8 Transformation" on page 25).

8.3 Scalar Field Object Commands

Commands directed against a scalar field object are issued as

Syntax: .scal.obj command [parameters]

Following is a list of all scalar field 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 (see "5.1.5 Modifying Objects" on page 23).

Syntax: .scal.obj renew [-selection SEL] [-set SET]

Example: .map.m renew -set level=1.2s, size=50, color=blue

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 "4.12 The GUI" on page 20)

Syntax: .scal.obj show
        .scal.obj hide

set get : modify or retrieve scalar field object properties (See Table 15 (P. 38) and see "5.1.5 Modifying Objects" on page 23)

Syntax: .scal.obj get P
        .scal.obj set PV [-selection SEL] [-range [src=SRC][,PROP=prop][val=VAL1:VAL2]]

render : modifies the graphical appearance of an object (see "8.4 Render & Graphical Appearance" on page 40)

8.4 Render & Graphical Appearance

The command render modifies the graphical appearance of a scalar field dataset object:

Syntax: .scal.obj render PV [,PV ...]

The render properties that can be used for the scalar field dataset objects are given in Table 17 (P. 41). Depending on the object type (contour or grid ), different rendering modes are available, specified as:

Syntax: .scal.obj render MODE

where mode is one of:

dot : (for type contour ) vertices are displayed as points only
line : (for type contour ) default mode, faces are outlined
fill : (for type contour ) faces are filled and lit
on / off : (for type grid ) turns rendering on (spheres) or off (points)

Material parameters can be modified with the command material (see "5.1.6 Graphical Appearance" on page 24).

8.5 Mapping Scalar Fields to Surfaces

DINO provides an easy way to map scalar field values to a surface. This can be accomplished by using the surface object command set with -range and as src the scalar field. Following is a generic example, assuming a surface named surf and an electrostatic potential as a scalar field dataset called pot

// load surf ...
// load pot ...
.surf new -name all            // generate surface object
.surf.all set color=red:white -range src=.pot, val=-5:0
.surf.all set color=red:red   -range src=.pot, val=-999:-5
.surf.all set color=white:blue -range src=.pot, val= 0:5
.surf.all set color=blue:blue -range src=.pot, val=5::999

Scalar Field Dataset Object Render Properties
Property	C7	G8	Description	Default
fast	X	X	turns off point and line antialiasing to increase drawing speed
light1	X		lighting is only applied to the front face, leaving the backside practically unlit and dark
light2	X		lighting is applied to both sides of the surface	X
lw	X		linewidth	1.0
nice	X	X	turns on point and line antialiasing	X
ps	X	X	pointsize	1.0
t	X		transparency, 1.0 is opaque, 0.0 is fully transparent	1.0

1. indicates that this property can be modified with set

2. indicates that this property can be modified with get

3. indicates that this property can be modified with set

4. indicates that this property can be modified with get

5. indicates a selectable property

6. inidicates a property that can be used in a range statement

7. applicable to object type contour

8. applicable to object type grid