Glossary
Maestro 10.2 User Manual
445
selection—(1) A group of atoms in the Workspace that has been picked or otherwise chosen.
The selection is highlighted by markers when the appropriate option is selected. (2) A group of
entries in the Project Table. The entries are highlighted in the table.
shortcut menu—The menu that is displayed when you right-click and hold on a component of
a panel, such as the sequence viewer in the main window.
startup directory—The directory from which
Maestro was started, on Linux (or from the
command line on Mac). On Windows and Mac, there isn’t a concept of a startup directory for
an application, so it is set to the Schrodinger folder in your Documents folder.
synchronization—updating the project with changes made in the Workspace. The default is to
perform synchronizations automatically.
user profiles directory—the directory (folder) in which Maestro profiles are kept for a
specific user.
user resources directory—the directory (folder) in which resource files are kept for a specific
user.
volume—a set of data points on a three-dimensional grid for a property
that is a function of the
three spatial coordinates.
working directory—
see
current working directory
.
Workspace—The open area in the center of the Maestro main window in which structures are
displayed.
Linux, Mac:
$HOME/.schrodinger/maestro
vv/profiles
Windows:
%APPDATA%\Schrodinger\maestrovv\profiles
Linux, Mac:
$HOME/.schrodinger
Windows:
%APPDATA%\Schrodinger
Maestro 10.2 User Manual
447
Index
Numerics
2D Sketcher dialog box.....................................
89
2D structures
displaying in Project Table ...............
185
,
194
exporting images of ..................................
223
exporting to SD file ..................................
223
options for 2D Viewer ..............................
223
Project Table preferences .........................
369
2D Viewer panel .............................................
222
A
active atom, changing .......................................
88
Add Definition dialog box ..............................
283
Add Hydrogens - Advanced panel ..................
109
Add Label Fields dialog box...........................
164
Add Property panel .........................................
228
Adjust panel ....................................................
100
Advanced Transformations panel ...................
105
aliases..............................................................
394
Align Atoms panel ......................................
66
,
68
alignment
of atoms to axis or plane.............................
65
of numbers and text in Project Table ........
346
of structures to a reference structure ........
254
alternate positions
displaying ...........................................
28
,
153
PDB import color code...............................
50
reading from PDB file ................................
43
switching between ......................................
28
transforming atoms with...................
106
,
351
ambient lighting ..............................................
146
ambient occlusion .............................................
78
angles
adjusting ...................................................
101
measuring .................................................
250
animation ........................................................
349
Appearance panel
Effects tab .................................................
148
Fog tab ........................................................
77
Lighting tab ..............................................
146
Materials tab .............................................
147
Perspective tab ............................................
76
Stereo tab ....................................................
75
Application Tree panel........................................
8
ASD ................................................................
443
ASL .................................................................
443
Atom and Bond Coloring panel ......................
134
atom labels
adding user text to ....................................
165
appearance ................................................
360
applying ....................................................
164
color..........................................................
360
composing ................................................
162
including descriptions in ..........................
360
moving......................................................
165
placement .................................................
360
removing...................................................
164
updating ....................................................
164
Atom Labels panel ..........................................
163
atom selection
adding to ...........................
119
,
120
,
122
,
123
by property ...............................................
126
by proximity .............................................
128
examples ...................................................
130
storing and retrieving................................
131
Atom Selection dialog box .............................
125
atom types (MacroModel)
setting .......................................................
110
table ..........................................................
424
united, option for use................................
372
atoms
active, changing ..........................................
88
adding to selection..............
28
,
119
,
122
,
123
aligning to axis or plane .............................
65
assigning residue number .........................
116
changing element........................................
95
coloring all................................................
134
coloring with schemes ..............................
135
deleting .....................................................
117
displaying or undisplaying .......................
150
dummy..............................................
117
,
254
finding ........................................................
36
hydrogen, adding ......................................
108
labeling .....................................................
162
molecular representation ..........................
142
moving..................................................
80
,
88
names........................................................
112
removing from selection...........................
119
retyping.......................................................
95
selecting for measurements ......................
250
valency violation ........................................
87
Auto-Help facility ...........................................
410
axes, displaying coordinate.............................
171