Prime User Manual - ISP

Contents
5.3 Running the Build Structure Job.......................................................................... 38
5.4 Saving and Exporting Built Structures ............................................................... 40
5.5 Technical Notes for the Build Structure Step..................................................... 40
Chapter 6: Fold Recognition ......................................................................................... 43
6.1 Overview of the Fold Recognition Step .............................................................. 43
6.2 Producing an SSP Profile ...................................................................................... 43
6.2.1 Importing and Exporting SSPs.......................................................................... 43
6.2.2 Generating SSPs .............................................................................................. 44
6.2.3 Editing or Deleting SSPs................................................................................... 45
6.2.4 Resetting SSPs................................................................................................. 46
6.3 Searching for Templates ........................................................................................ 46
6.3.1 Search Program Options .................................................................................. 46
6.3.2 Search Program Technical Details.................................................................... 47
6.3.3 Search Output................................................................................................... 47
6.4 Evaluating Templates ............................................................................................. 49
6.5 Building a Model...................................................................................................... 50
Chapter 7: Prime–Refinement..................................................................................... 51
7.1 Preparing Structures for Refinement .................................................................. 51
7.2 Using the Refinement Panel.................................................................................. 55
7.3 Setting Up an Implicit Membrane ......................................................................... 56
7.4 Prime Energy Analysis ........................................................................................... 58
7.5 Refining Loops ........................................................................................................ 58
7.6 Predicting Side Chains........................................................................................... 61
7.7 Minimizing Structures ............................................................................................ 62
7.8 Refinement Panel Options..................................................................................... 63
7.8.1 General Options................................................................................................ 63
7.8.2 Dielectric Options.............................................................................................. 64
Prime 2.1 User Manual v