GaussView 5
Reference
Æleen Frisch
Hrant P. Hratchian
Roy D. Dennington II
Todd A. Keith
John Millam
with
Alice B. Nielsen
Andrew J. Holder
Joanne Hiscocks
Gaussian, Inc.
340 Quinnipiac Street, Building 40
Wallingford, CT 06492 USA
www.gaussian.com
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Copyright 1997-2009, Gaussian, Inc.
Portions Copyright 1997-2009, Semichem, Inc.
All Rights Reserved.
ISBN: 978-1-935522-00-3
Manual Version 5.0 corresponding to GaussView version 5.0.
June, 2009
Updated on: 9 Jun 2009
GaussView 5 Reference iii
Table of Contents
List of Figures ........................................................................................vii
Introduction .......................................................................................... 1
Typographic Conventions........................................................................... 1
GaussView Basics ...................................................................................... 2
Molecules, Molecule Groups and Views .................................................................. 3
Customizing MultiView Windows ................................................................... 5
Animating Multiple Structures....................................................................... 6
Using the Mouse ...................................................................................... 6
Limiting Mouse Actions to One Fragment ............................................................6
GaussView Menus..................................................................................... 7
Table of Icons and Menu Items ......................................................................... 7
GaussView Preferences ...............................................................................12
Specifying GaussView Window Behavior............................................................. 13
Modifying Icon Sizes ..............................................................................13
Displaying GaussView Tips............................................................................ 14
Building Molecules ...................................................................................15
Placing Elements and Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
e Element Fragments Palette .....................................................................15
e R-Group Fragments Palette..................................................................... 16
e Rings Palette..................................................................................16
e Biological Fragments Palette .................................................................... 17
Making Palettes Sticky..........................................................................17
Placing a Fragment in a Centroid Position ...........................................................17
Undo and Redo...................................................................................18
Viewing and Adjusting Structure Parameters ............................................................18
Inquire Mode.....................................................................................18
Semichem SmartSlides............................................................................. 19
e Bond SmartSlide ...........................................................................19
e Angle and Dihedral SmartSlides .............................................................20
Adding and Deleting Valences ...................................................................... 21
Invert About Atom (Mirror Invert).................................................................. 22
Cleaning Structures ............................................................................... 22
Clean Performance Tips ........................................................................24
Rebonding Structures..............................................................................24
Imposing Symmetry ...............................................................................24
All About Selections: From Atoms to Fragments, Residues, Chains and Beyond ..............................26
Selection-Related Toolbar Icons..................................................................... 26
Selection Keystrokes in View Windows ...........................................................26
Selecting with the Atom List Editor and Similar Tools .................................................26
Using the Atom Group Editor ......................................................................27
e Atom Selection Editor .........................................................................28
Advanced Building Features ...........................................................................29
Using a Custom Fragment Library ..................................................................29
e Atom List Editor ..............................................................................30
Using Sublist Filters ............................................................................33
Dening Isotope Masses and Isotopologues ....................................................... 34
e PDB Residue Editor and e PDB Secondary Structure Editor ......................................34
