Prime User Manual - ISP

Contents
Document Conventions ..................................................................................................... ix
Chapter 1: Introduction ....................................................................................................... 1
1.1 The Prime Suite in Maestro ..................................................................................... 1
1.2 Prime Documentation............................................................................................... 2
1.3 Running Schrödinger Software .............................................................................. 3
1.4 Citing Prime in Publications.................................................................................... 3
Chapter 2: Using Prime–Structure Prediction .................................................... 5
2.1 Prime Runs and Maestro Projects.......................................................................... 5
2.2 General Panel Layout................................................................................................ 7
2.3 The Prime Menu Bar ................................................................................................. 9
2.3.1 The File Menu ..................................................................................................... 9
2.3.2 The Edit Menu................................................................................................... 10
2.3.3 The Display Menu ............................................................................................. 10
2.3.4 The Step Menu ................................................................................................. 12
2.4 The Prime Toolbar ................................................................................................... 13
2.5 Prime Job Options and Control ............................................................................ 14
2.5.1 The Job Options Dialog Box ............................................................................. 14
2.5.2 Setting Up and Launching Jobs ........................................................................ 14
2.5.3 Monitoring Jobs................................................................................................. 15
2.5.4 Adding Structures to the Project Table.............................................................. 16
Chapter 3: Prime–Structure Prediction: Initial Steps ................................... 17
3.1 Input Sequence Step............................................................................................... 18
3.2 Find Homologs Step ............................................................................................... 19
3.2.1 Importing Homologs.......................................................................................... 19
3.2.2 Searching for Homologs.................................................................................... 20
3.2.3 Find Homologs Search Options ........................................................................ 21
3.2.4 Search Results.................................................................................................. 22
Prime 2.1 User Manual iii