Contents
Release 2005, March 2005
1. Introduction
- What Does Search_Compare Do?
- Starting Search_Compare
- Using This Guide
- Additional Information
- Note on Command Names
2. Theory
- Superimposing Molecules
- RMS Fitting
- Electrostatic Potential Similarity
- Steric Shape Similarity
- Field_Fit (Electrostatic & Steric Similarity)
- Steric Clash-checking
- Systematic Conformational Searching
- Standard Searches
- Use of Distance Constraints
- Distance Maps
- Distance Maps used in Series
- Screening by Energy Criteria
- Vector Maps
- Screening Duplicate Conformations
3. Implementation
- Volumes
- Overlapping Molecules
- Systematic Conformational Searching on Ring Systems
- Use of Energy Criteria in Systematic Conformational Searching
- Vector Mapping
- Background Jobs
4. Command Summary
- Volume Pulldown
- Create
- Boolean
- Grid_Setup
- Align
- Color
- Label
- Display
- List
- Overlap Pulldown
- Define
- Field_Fit
- Display
- SC_Search Pulldown
- Set_Ring_Closure
- Set_Rot_Bond
- Set_Distance
- Set_Dist_Map
- Scale_Radii
- Set_Energy_Params
- Set_Filter_Params
- SCS_Run
- Load
- Vector_Map Pulldown
- Create
- Color
- Label
- Display_Vector
- List
- Conformer Pulldown
- Display
- Distance_Map Pulldown
- Boolean
- Construct_Graph
- Spreadsheet Pulldown
- Graph Pulldown
- Background_Job Pulldown
5. Methodology
- Using the Volume Pulldown
- Aligning Molecules and Volumes
- Specifying How Volumes will be Calculated
- Creating Volumes
- Preparing the System
- Specifying the Volume's Size
- Setting Whether and How a Volume Is Displayed
- Calculating the Volume
- Displaying Information About the Volume
- Boolean Operations on Volumes
- Determining How Many Volumes Are Displayed after a Boolean Operation
- Changing How Existing Volumes Are Displayed
- Cancelling a Volume Calculation
- Using the Overlap Pulldown
- Using Highlights
- Defining Atom Pairs
- Setting Up Torsions
- Checking the Specifications
- Correcting Mistaken Entries
- Executing the RMS Fitting Calculation
- Executing the Field Fitting Calculation
- Using the SC_Search Pulldown
- Standard Searches
- Setting up Parameters for the Standard Search and Background Job
- Defining the Bonds to be Rotated
- Scaling Atomic Radii
- Setting Distance Constraints
- Setting Up the Background Job
- Running the Background Job for Standard Searches
- Initiating the Search
- Monitoring the Job
- Killing a Background Job
- Loading Search Results into Insight II
- Advanced Searches
- Setting up an Advanced Search and Background Job
- Setting up Distance Map Calculations
- Setting up Energy Calculations
- Initiating the Background Job for Advanced Searches
- Using the Distance_Map Pulldown
- Boolean Operations on Distance Maps
- Setting up a Boolean Distance Map Calculation
- Visualizing a Distance Map as a Graph
- Constructing a Distance Map Graph of an N-Dimensional Distance Map
- Constructing a Distance Map Graph From a Trajectory.
- Using the Vector_Map Pulldown
- Creating and Editing a Vector Map
- Controlling the Display of a Vector Map
- Using the Conformer Pulldown
- Displaying Desired Conformers
- Saving and Using Lists of Conformers
- Manipulating the List of Conformers
6. Tutorial
- Pilot Online Tutorials
A. References
B. Glossary
C. File Formats
- Input Files
- Search_Compare Parameter File (.scs_prm)
- Format of Search_Compare Parameter File
- Example Search_Compare Parameter File
- Output Files
- Search_Compare Log File (.scs_log)
- Files Used and Produced by Advanced Searches
D. Utilities
- scs_xdrtor
- Purpose
- Syntax
- Errors and Warnings
Last updated November 22, 2003.
Copyright © 2003, Accelrys Inc. All rights
reserved.