Contents
Schrödinger Software Release 2015-2
vi
5.7
Changing the Bond Order and Formal Charge
.................................................. 96
5.8
Connecting or Fusing Structures
......................................................................... 97
5.9
Adjusting the Geometry
......................................................................................... 99
5.9.1
Adjusting Distances, Angles, and Dihedral Angles ........................................... 99
5.9.1.1
Using the Workspace Tools
.................................................................... 99
5.9.1.2
From the Adjust Panel
.......................................................................... 100
5.9.1.3
Repeating Adjustments
........................................................................ 101
5.9.2
Adjusting Peptide Linkages and Side Chains ................................................. 101
5.9.3
Adjusting the Stereochemistry ........................................................................ 103
5.9.4
Adjusting Groups of Atoms ............................................................................. 104
5.9.5
Structure Sculpting.......................................................................................... 107
5.9.6
Cleaning Up the Geometry ............................................................................. 107
5.10
Adding and Treating Hydrogen Atoms
............................................................ 108
5.11
Changing Atom Properties
................................................................................ 110
5.11.1
Atom type (MacroModel)............................................................................... 110
5.11.2
Partial Charge ............................................................................................... 111
5.11.3
PDB Atom Name........................................................................................... 111
5.11.4
Atom Name ................................................................................................... 112
5.11.5
Grow Name ................................................................................................... 113
5.11.6
Isotope Number ............................................................................................ 113
5.11.7
Other Properties ........................................................................................... 114
5.12
Changing Residue Properties
........................................................................... 115
5.13
Defining Dummy Atoms
..................................................................................... 117
5.14
Deleting Atoms and Bonds
............................................................................... 117
Chapter 6:
Selecting Atoms
........................................................................................ 119
6.1
Picking in the Workspace
.................................................................................... 119
6.2
Using the Toolbar Buttons
................................................................................... 119
6.3
Using the Picking Tools
....................................................................................... 121
6.3.1
The Pick Option Menu .................................................................................... 123
6.3.2
The Dihedral Selection Dialog Box ................................................................. 124
Maestro 10.2 User Manual
vii
6.4
Using the Edit Menu
.............................................................................................. 125
6.5
The Atom Selection Dialog Box
.......................................................................... 125
6.5.1
Selecting Atoms by Property........................................................................... 126
6.5.2
Selecting Atoms by Connectivity..................................................................... 127
6.5.3
Selecting Atoms Using Previously Defined Sets or Selections ....................... 127
6.5.4
Combining and Modifying Atom Selections .................................................... 127
6.5.5
Selecting Atoms by Proximity.......................................................................... 128
6.5.6
Editing and Storing Expressions ..................................................................... 129
6.5.7
Converting Expressions to Lists...................................................................... 129
6.5.8
Examples of Atom Selection ........................................................................... 130
6.6
Storing the Workspace Selection
....................................................................... 131
Chapter 7:
Changing the Appearance of Structures
.................................. 133
7.1
The Representation Toolbar
................................................................................ 133
7.2
Changing Atom, Bond, and Background Color
............................................... 134
7.2.1
Applying a Single Color to Atoms and Bonds ................................................. 134
7.2.2
Coloring Bonds by Atom Colors ...................................................................... 135
7.2.3
Using Color Schemes to Color Atoms ............................................................ 135
7.2.4
Creating and Editing Color Schemes.............................................................. 138
7.2.5
Setting the Background Color ......................................................................... 141
7.3
Changing Molecular Representations
............................................................... 141
7.3.1
Changing the Representation of Atoms And Bonds ....................................... 141
7.3.2
Rendering Proteins, DNA, and RNA as Ribbons ............................................ 143
7.4
Changing Lighting, Materials, and Special Effects
......................................... 145
7.5
Displaying and Undisplaying Atoms
................................................................. 150
7.5.1
The Display Atoms Toolbar ............................................................................. 150
7.5.2
Selectively Displaying Atoms .......................................................................... 150
7.5.3
Displaying Periodic Structures ........................................................................ 152
7.6
Display Styles
........................................................................................................ 154
7.6.1
Applying the Workspace Style ........................................................................ 155
7.6.2
Defining the Workspace Style ......................................................................... 156