NOC (current version 1.5.2.10) is a free program for protein structure model-building, visualization, validation and analysis ...
Some features of NOC:
Auto-fit residues' side-chain against density data;
Solid surface generation and electrostatic potential, hydrophobic force coloring;
Potentials calculations;
Customize molecular electronic density map contouring;
Easy to add/delete HOH, heteroatom Group, residue;
Real 3D Stereo Visualizing Support (need a Quad Buffer Graphic Adapter and a Stereo Glasses);
Easy to make a animate stream of molecular model;
WYSIWYG Labeling method;
Easy to compare similar structures;
Auto structure checking and hydrogen atoms adding;
Predict possible motifs (sites) in the molecule;
Auto-determinate secondary structures;
Build related molecules and contacts according to molecular crystallographic symmetries;
Calculate molecular accessible surface, embedded surface, residue accessibility;
Details of Heteroatom interactions in the molecule;
Details of Hydrogen bonds in the molecule;
Validate structure on the fly;
More precise ribbon model representation ;
Novel Cartoon model representation ;
High quality rendering and many types of output (such as TIFF, PNG, BMP, PS…) ;