Maestro User Manual
Schrödinger Software Release 2015-2
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- Schrödinger Software Release 2015-2 448 Index
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
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
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