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


Structure Dataset

A small script to get started with the structure dataset
Download this tutorial: struct.tar.gz
// example using IIB subunit of the fructose transporter
// Schauder et. al. 1997

// define secondary structure
set helix rnum=18:26,36:40,42:49,63:71,88:96,125:136,154:159 
set strand rnum=57:61,30:34,79:84,3:10,102:107,140:143

// load pdb file, a dataset named iib will be created
load iib.pdb

// set the secondary structure, default is coil
.iib set rtype=helix -sel $helix
.iib set rtype=strand -sel $strand

// create an object containing all atoms 
// (selection ommited, defaults to *)
.iib new -name all

// center on this object
scene center [.iib.all]

// adjust the clipping planes
scene autoslab
scene set near-=5,far+=5

// change rendering mode
.iib.all render cpk,detail=3
.iib.all render custom,bw=0.2,sr=0.2,detail=3,detail2=2
.iib.all render simple,lw=2

// change coloring, e.g. of carbon atoms
.iib.all set color=yellow -sel ele=C

// hide this object and create CA trace
.iib.all hide
.iib new -name ca -type trace

// color helix and strand residues differently
.iib.ca set color=green -sel $strand
.iib.ca set color=purple -sel $helix

// since sec structure was defined above,
// render it this way
.iib.ca render hsc

// other rendering modes
.iib.ca render sline
.iib.ca render tube
.iib.ca render custom
.iib.ca render simple