Getting Started
-Structure Dataset
-DNA rendering
-Surface Dataset
-Scalar Field Dataset: X-ray
-Scalar Field Dataset: EM
-Topograph Dataset
-Electrostatic Potential I
-Electrostatic Potential II
-Geometric Primitives
-Stereo output
-Saving the viewing matrix


Scalar Field Dataset: X-ray

An electron density map used in x-ray crystallography is very easy to display with DINO. In contrast to other datasets, a few properties need to be defined during object creation (otherwise defaults will be used), such as center of the map (default {0,0,0}), the size (default 30) and the contour level (default 0). Appending the letter 's' to the contour level means sigma units.

Download this tutorial: scal_xray.tar.gz
// example using IIB subunit of the fructose transporter
// Schauder et. al. 1997

// preset CS so that script works
set CS .iib:15.CA
// load the structure dataset
load iib.pdb
// load the scalar field dataset 
// (in this case a CCP4 electron density map)
load iib_2fofce.map -name m

// generate structure object and center on it
.iib new -name all
scene center [.iib.all]

// adjust the clipping planes
scene autoslab

// create a new map object, centered on structure object,
// contour level 1sigma unit, 20x20x20 grid units in size
.m new -name m -set center=[.iib.all],level=1.0s,size=20
.m.m set color=aquamarine

// to recenter the map on another point, select an atom
// with the mouse and then use
.m.m renew -set center=[$CS]
scene center [$CS]

// to restrict the map around certain regions, use the 
// within operator

// create a new structure object, in this case
// only residue H15
.iib new -name h15 -sel rnum=15

// renew the map with a selection statement
// to cover only residue 15
.m.m renew -sel 2.2<>.iib.h15

// to remove the selection criteria use
.m.m renew -sel *