Maestro User Manual
Schrödinger Software Release 2015-2
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- Schrödinger Software Release 2015-2 452 Index
Schrödinger Software Release 2015-2 452 Index isosurface ........................................................ 297 isovalue ........................................... 297 , 309 , 443
hydrophobic/philic map defaults .............. 305
restrictions on changing............................ 307
J Jaguar files, importing ...................................... 51 Jaguar plot files, importing ............................. 306 job directory .................................................... 443 jobs
file deletion ............................................... 377
from renamed projects.............................. 175
monitoring ................................................ 375
output incorporation ......................... 180
, 374
status feedback in Workspace................... 359
joining geometry, specifying............................. 86
KNIME running workflows from Maestro............. 389 sending and receiving structures .............. 403
Label All button .............................................. 165 labels
adding user text to .................................... 165
appearance ................................................ 360
applying ............................................ 164
, 166
color.......................................................... 360
displaying for hidden atoms ..................... 360
field descriptions in .................................. 360
moving ...................................... 165
, 167
, 254
placement.................................................. 360
removing........................................... 164
, 166
repositioning ............................................. 165
updating ............................................ 164
, 166
launch directory ........................................ 11 , 444 ligand .............................................................. 444 ligand detection settings.................................. 370 Ligand Filtering panel..................................... 279 Ligand Interaction Diagram panel .................. 274 Limit panel, surfaces....................................... 310 local transformations............................... 104 – 106 exiting mode temporarily ......................... 106
translations................................................ 105
log file, Maestro .............................................. 340
M macros
creating ..................................................... 395
installing ................................................... 386
Macros panel................................................... 396
Maestro command language................................... 390 commands, running .................................... 16 file format ................................................. 417 file format example................................... 419 help ........................................................... 407 log file....................................................... 340 main window ........................................ 14 ,
menus ................................................... 16 – 17 quitting ....................................................... 38 starting ........................................................ 12 workflow paradigm ...................................... 5 Maestro resources directory............................ 444 main window..................................................... 15 components, hiding and showing ............... 15 Manage Custom Property Families panel....... 242 Manage Highlights panel ................................ 168 Manage Plots panel......................................... 286 Manage Scenes panel...................................... 181 Manage Scripts panel...................................... 387 Manage Surfaces panel ................................... 308 manuals, searching.......................................... 411 Mark property ................................................. 220 markers
displaying ................................................. 249
H-bond, halogen bond, contact, pi interaction.......................................... 252 measurement, geometric........................... 250 marking entries ............................................... 220 measurements angles........................................................ 250
creating properties for .............................. 253
creating properties from ........................... 253
decimal places .......................................... 361
dihedrals ................................................... 250
distances ................................................... 250
dummy atoms ........................................... 254
H-bond and contact .................................. 251
label format ...................................... 254
, 361
moving labels ........................................... 254
writing to a file ......................................... 253
Measurements panel ....................................... 250
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