Contents
Schrödinger Software Release 2015-2
xii
10.7
Assigning Bond Orders and Partial Charges
................................................. 278
10.8
Ligand Filtering
.................................................................................................... 279
10.8.1
Selecting a Structure Source ........................................................................ 280
10.8.2
Defining the Matching Method ...................................................................... 281
10.8.3
Defining Matching Criteria ............................................................................ 281
10.8.4
Defining New Matching Patterns................................................................... 282
10.8.5
Eliminating Duplicate Ligands....................................................................... 283
10.9
Minimizing Structures
........................................................................................ 284
10.10
Visualization Tools
............................................................................................ 284
Chapter 11:
Plotting
.......................................................................................................... 285
11.1
Scatter Plots
......................................................................................................... 285
11.1.1
Managing Plots ............................................................................................. 285
11.1.2
Creating Plots .............................................................................................. 286
11.1.3
Changing Plot Settings ................................................................................. 287
11.1.3.1
Changing the Plotted Properties
......................................................... 287
11.1.3.2
Changing the Plot Symbols and Lines
................................................. 288
11.1.3.3
Changing the Axis and Color Scale Settings
........................................ 288
11.1.3.4
Changing the Plot Shape and Area
..................................................... 290
11.1.3.5
Adding a Title and a Legend
............................................................... 290
11.1.3.6
Labeling Plot Points
........................................................................... 290
11.1.4
Changing the View of a Plot.......................................................................... 291
11.1.5
Interacting with the Project Table .................................................................. 291
11.1.6
Saving Plot Images ....................................................................................... 292
11.2
Plotting Coordinate Scan Results
.................................................................... 292
11.2.1
General Features of Coordinate Scan Plot Panels ....................................... 293
11.2.2
The Plot of One-Coordinate Scan Panel....................................................... 294
11.2.3
The Plot of Two-Coordinate Scan Panel ....................................................... 296
Chapter 12:
Surfaces
....................................................................................................... 297
12.1
Generating Surfaces
........................................................................................... 297
12.1.1
Surface Generation Controls......................................................................... 297
Contents
Maestro 10.2 User Manual
xiii
12.1.2
Molecular Surfaces ....................................................................................... 299
12.1.3
Extended Radius Surfaces............................................................................ 300
12.1.4
Van der Waals Surfaces................................................................................ 301
12.1.5
Electrostatic Potential Surfaces .................................................................... 301
12.2
Hydrophobic/philic Surfaces
............................................................................. 302
12.2.1
Background ................................................................................................... 303
12.2.2
Mapping Algorithm ........................................................................................ 304
12.2.3
Specifying a Structure to Be Mapped ........................................................... 305
12.2.4
Defining the Mapping Box ............................................................................. 305
12.2.5
Running the Job............................................................................................ 306
12.2.6
Viewing the Surface ...................................................................................... 306
12.3
Importing Surface or Volume Files
.................................................................. 306
12.4
The Manage Surfaces Panel
.............................................................................. 307
12.4.1
Importing, Modifying, and Deleting Surfaces ................................................ 309
12.4.2
Changing the Appearance of the Surface .................................................... 310
12.4.2.1
Style and Transparency
..................................................................... 311
12.4.2.2
Color Scheme
.................................................................................... 312
12.4.2.3
Depth Perception
............................................................................... 313
12.4.3
Displaying Volumes....................................................................................... 313
12.4.4
Exporting Surfaces........................................................................................ 315
Chapter 13:
Customizing Maestro
.......................................................................... 317
13.1
Changing and Saving Panel Layout
................................................................. 317
13.2
Customizing the Menus and Keyboard Shortcuts
........................................ 318
13.3
Customizing Mouse Actions
............................................................................. 321
13.4
Customizing Profiles
.......................................................................................... 323
13.5
Customization by Editing Resource Files
...................................................... 324
13.5.1
Visual Style Resources ................................................................................. 325
13.5.2
Color Definitions............................................................................................ 325
13.5.3
Color Schemes ............................................................................................. 326
13.5.3.1
The scheme.res File
........................................................................... 326
13.5.3.2
Color Scheme Files
............................................................................ 326