Contents
Schrödinger Software Release 2015-2
x
9.6.13
Ranking and Sorting Entries by Rank ........................................................... 214
9.6.14
Recording a Movie from Selected Entries..................................................... 216
9.7
The ePlayer
............................................................................................................. 216
9.7.1
ePlayer Modes ................................................................................................ 217
9.7.2
ePlayer Options............................................................................................... 218
9.8
Viewing Poses
........................................................................................................ 220
9.9
Viewing 2D Structures
.......................................................................................... 220
9.9.1
Displaying 2D Structures in the Project Table ................................................. 220
9.9.2
The 2D Viewer Panel ...................................................................................... 221
9.10
The Entry List Panel
............................................................................................ 224
9.11
Entry Properties
.................................................................................................. 226
9.11.1
The Stars and Mark Properties..................................................................... 227
9.11.2
The Date Added and Date Modified Properties ............................................ 227
9.11.3
Creating New Properties............................................................................... 228
9.11.3.1
Adding Properties with a Default Value
............................................... 228
9.11.3.2
Adding Properties by Copying
............................................................ 228
9.11.3.3
Calculating Properties from Structural Data
......................................... 228
9.11.3.4
Calculating Properties from Other Properties
...................................... 231
9.11.4
Editing Properties ......................................................................................... 233
9.11.5
Copying Properties ....................................................................................... 233
9.11.6
Merging Properties ....................................................................................... 235
9.11.7
Setting the Number of Decimals and the Notation for a Real Property......... 236
9.11.8
File Name Properties .................................................................................... 236
9.11.9
Renaming Properties .................................................................................... 237
9.11.10
Deleting Properties ..................................................................................... 238
9.11.11
Clearing Property Values ............................................................................ 238
9.11.12
Showing and Hiding Properties .................................................................. 239
9.11.12.1
Using the Properties Menu
............................................................... 239
9.11.12.2
Using the Property Tree
.................................................................... 240
9.11.13
Creating and Editing Custom Property Families ......................................... 241
9.11.14
Coloring Table Cells By Property Value ...................................................... 244
9.11.15
Moving, Reordering, and Resizing Property Columns ................................ 246
9.11.16
Exporting and Importing Data ..................................................................... 248
Contents
Maestro 10.2 User Manual
xi
Chapter 10:
Tools
............................................................................................................... 249
10.1
Displaying Markers
............................................................................................. 249
10.2
Displaying Measurements in the Workspace
................................................. 249
10.2.1
Measuring Distances, Angles, Dihedrals, and NMR Coupling ...................... 250
10.2.2
Displaying Nonbonded Interactions .............................................................. 251
10.2.3
Displaying H-H NMR Coupling Constants..................................................... 252
10.2.4
Storing the Results of Measurements........................................................... 253
10.2.5
Defining Dummy Atoms for Measurements .................................................. 254
10.2.6
Positioning and Formatting Measurement Labels......................................... 254
10.3
Superimposing and Aligning Structures
........................................................ 254
10.3.1
The Superposition Panel............................................................................... 255
10.3.2
The Flexible Ligand Alignment Panel............................................................ 257
10.3.3
Aligning Centers of Mass .............................................................................. 259
10.3.4
Aligning Proteins ........................................................................................... 259
10.4
Using Atom Sets
.................................................................................................. 259
10.4.1
Creating and Deleting Sets ........................................................................... 260
10.4.2
Selecting Atoms for a Set.............................................................................. 260
10.4.3
Reading and Writing Sets ............................................................................. 261
10.4.4
Selecting Atoms in the Workspace that Match a Set .................................... 261
10.5
Ligand Analysis Tools
........................................................................................ 261
10.5.1
R-Group Analysis.......................................................................................... 261
10.5.2
Scaffold Decomposition ................................................................................ 262
10.6
Protein Tools
........................................................................................................ 265
10.6.1
Assigning Protein Secondary Structure ........................................................ 265
10.6.2
Viewing Reports on Protein Properties......................................................... 265
10.6.3
Protein Reliability Reports ............................................................................ 267
10.6.4
Ramachandran Plots .................................................................................... 270
10.6.5
Energy Profiles of Torsional and Rotamer States ......................................... 272
10.6.6
Ligand Interaction Diagrams ......................................................................... 274
10.6.7
Protein Splicing ............................................................................................. 276
10.6.8
The Multiple Sequence Viewer ..................................................................... 278