Manual

Table of Contents:

Quick Index:

• Starting UltraScan
• UltraScanLicense Key Registration
• UltraScan Menu System
• UltraScan Configuration
• Editing Sedimentation Data
• Velocity Data Analysis
• Equilibrium Data Analysis
• Nonlinear Least Squares Analysis
• Monte Carlo Analysis
• UltraScan Utilties
• UltraScan Simulation Programs (Including US-SOMO)
• UltraScan Database Frontend
• Additional Information

• Editing Sedimentation Data:

  Velocity Data:

  • Editing Absorbance Velocity Data
  • Editing Interference Velocity Data
  • Run Diagnostics and Details
  • Reviewing Dataset Information

  Equilibrium Data:

  • Editing Absorbance Equilibrium Data
  • Editing Interference Equilibrium Data
  • Run Diagnostics and Details
  • Reviewing Dataset Information

  All Sedimentation Data:

  • Editing Spikes, Scratches, etc. from Experimental Data
  • Editing the cell contents description
  • Exporting Sedimentation Data
  • Printing Sedimentation Data (experimental data only, check here for printing analysis results)

• Velocity Data Analysis:

  van Holde - Weischet Analysis:

  • van Holde - Weischet Analysis
  • Enhanced van Holde - Weischet Analysis
  • Combining Integral Distribution (G(s)) Plots
  • van Holde - Weischet Tutorial
  • van Holde - Weischet Data Interpretation

  Finite Element Analysis:

  • Finite Element Analysis
  • Model Selection
  • Finite Element Model Control
  • Finite Element Fitting Control
  • Finite Element Tutorial
  • Finite Element Results Interpretation

  Other Analysis Methods:

  • 2-dimensional Spectrum Analysis
  • Genetic Algorithm Analysis
  • C(s) Analysis
  • Second Moment Analysis
  • Time Difference Analysis (dC/dt)
  • Radial Difference Analysis (dC/dr)

• Equilibrium Data Analysis:
  • Estimating Equilibrium Speed
  • LN(C) vs. R² Analysis

  • Global Nonlinear Least-Squares Equilibrium Analysis:
    • Setting up a fitting project
    • Model Selection
    • Scan Diagnostics
    • Scan Editing
    • Parameter Controls
    • Fitting Information
    • Model-Specific Information
      • Predefined Model Index
    • Equilibrium Analysis Tutorial

• Nonlinear Least Squares Analysis
  • Fitting Control Functions

• Monte Carlo Analysis:
  • Monte Carlo Analysis
  • Monte Carlo Statistics
  • Monte Carlo Tutorial
  • Monte Carlo Analysis using a Linux Beowulf Supercomputer

• Utilities
  • Data Archive Database
  • Re-order Scan File Sequences
  • Renaming cell content identifications in edited data
  • Exporting raw experimental data
  • Printing raw experimental data
  • Combine van Holde - Weischet G(s) Distributions
  • Combine molecular weight distributions from S20,W-corrected van Holde - Weischet G(s) Distributions
  • Generating html reports from analyzed data
  • Diagnostics
  • Calculate DNA/RNA Molecular Weights
  • Buffer Corrections
  • Calculate Protein Molecular Weight, Extinction coefficient at 280 nm and partial specific volume (v-bar) from protein sequence
  • Calculate Protein Extinction Profile
  • Linux System Utilities
  • Linux Beowulf Supercomputer Support
  • Color Configuration Utility
  • Font Configuration Utility
  • Administrator Password Utility

• Simulation Programs:
  • Finite Element Simulations of Velocity and Approch-to-Equilibrium Experiments
    • Finite Element Model Selection
  • Equilibrium Simulator
  • Estimate Equilibrium Times
  • Self-Association Simulator
  • Model s, D and f from MW for 4 basic shapes
  • Predict Molecular Dimensions from MW and s, MW and D, or s and D for 4 basic shapes
  • SOMO SOlution MOdeler

• UltraScan Database Frontend:
  • Introduction
  • MySQL Database Installation
  • Database Configuration
  • Committing Data to the Database
    1. Investigator contact information
    2. Buffer composition files for hydrodynamic corrections
    3. Peptide sequence files
    4. Nucleotide sequence files
    5. Experimental data (entire runs with associated data)

  • Retrieving Information from the Database
    1. Retrieve by Investigator Name
    2. Retrieve by Date
    3. Retrieve by experimental description
    4. Retrieve by experimental data type and optical system used

  • Initializing a new Database

• Additional Information
  • File Structure and File Formats
  • Printing
  • Customizing and generating Publication-Quality Graphs of all UltraScan Plots
  • Downloading/Upgrading UltraScan