Schrödinger Software Release 2015-2
448
Index
Axis Settings dialog box .................................
289
axis, aligning atoms to ......................................
65
B
Babel structure file format conversion
program....................................................
45
,
55
Ball & Stick representation
applying ....................................................
142
modifying .................................................
381
balloon help.............................................
338
,
410
Binding Site Surface Settings dialog box .......
160
bond labels
applying ....................................................
166
color..........................................................
361
moving ......................................................
167
removing...................................................
166
updating ....................................................
166
Bond Labels panel ..........................................
166
bond order
automatic assignment ...............................
278
changing .....................................................
97
increasing in Draw mode............................
88
bonds
adjusting ...................................................
101
changing order of........................................
96
displaying lengths for local
transformation .......................................
106
displaying order of....................................
380
representation ...........................................
142
smoothing of lines ....................................
380
zero-order .................................................
118
Build panel ........................................................
81
Atom Properties tab....................
95
,
110
–
113
Fragments tab .................................
82
,
85
,
87
Residue Properties tab ..............................
116
Build toolbar .....................................................
19
button menu ..............................................
17
,
443
button menu, item types....................................
17
C
Calculate Properties panel ..............................
229
calculator, Project Table..................................
231
Captions button ...............................................
167
captions, Workspace .......................................
167
centroid, defining ............................................
117
Centroids panel ...............................................
117
chain names ....................................................
116
charges, assigning ...................................
111
,
278
chiral atoms, labeling........................................
90
chirality, inverting .....................................
80
,
103
Choose Import Key dialog box .........................
59
Choose Profile dialog box.................................
14
cis-trans isomers, interconverting ...................
104
clearing the Workspace ...................................
204
clipboard, copying to ......................................
405
clipping planes ..........................................
72
,
443
and depth cues ............................................
78
automatic adjustment preference..............
351
hiding and redisplaying window ..............
394
moving........................................................
31
window .......................................................
15
zoom preference ...............................
352
,
353
Color By Property dialog box.........................
245
color ramp .......................................................
312
color
schemes
atom labels................................................
360
atoms ................................................
134
–
135
bond labels................................................
361
creating .............................................
138
,
140
customizing ......................................
138
,
326
deleting .....................................................
141
editing.......................................................
138
exporting...................................................
140
importing ..................................................
140
PDB import ................................................
50
resource files.............................................
326
ribbons ......................................................
144
surfaces.....................................................
312
Workspace background ............................
141
Color Schemes panel ......................................
138
columns, Project Table
aligning data .............................................
195
moving......................................................
246
resizing .....................................................
195
Command Aliases panel .................................
395
command aliases, creating ..............................
394
command completion........................................
16
command history ......................................
38
,
391
command input area..........................................
16
hiding........................................................
394
showing and hiding ....................................
15
using ...........................................................
38
command language, Maestro ..........................
390