Force Field

Explorer

A Graphical User Interface to TINKER

June 2004, Version 4.2

Table of Contents

Introduction. 4

Current Release. 4

Future Plans. 4

Installation. 5

· Linux. 5

· Macintosh OS X.. 5

· Microsoft Windows. 5

Description of Force Field Explorer Components. 7

Ø Molecular Tree. 7

Ø 3D Graphics and Global Axis. 8

Ø Keyword Editor. 9

Ø Modeling Commands. 10

Ø Logs. 11

Description of Force Field Explorer Menus. 13

Ø File. 13

¨ Open. 13

¨ Save As. 13

¨ Close. 13

¨ Close All 13

¨ Download from PDB.. 13

¨ Load Restart Data. 13

¨ Load Induced Data. 13

¨ Exit 13

Ø Selection. 13

¨ Select All 14

¨ Restrict to Selections. 14

¨ Highlight Selections. 14

¨ Set Selection Color 14

¨ Label Selected Atoms. 14

¨ Label Selected Residues. 14

¨ Set Label Font Size. 14

¨ Set Label Font Color 14

Ø Display. 14

¨ Wireframe. 15

¨ Tube. 15

¨ Spacefill 15

¨ Ball & Stick. 15

¨ Invisible. 15

¨ RMIN..