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Classroom Contents
Building a Graphical Interface for Exploring Protein Dynamics and Spectroscopy - PigmentHunter
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- 1 Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App.
- 2 Acknowledgements
- 3 Outline
- 4 PigmentHunter Interface and Workflow Applications and Examples
- 5 Motivation
- 6 Checklist:
- 7 PigmentHunter: The 'Point-and-Click' Simulation Tool
- 8 Background and Significance
- 9 An Overview of PigmentHunter's Workflow
- 10 Background and Significance
- 11 Main Window 1. Characterizing Pigments
- 12 nanoHub Embedded Libraries
- 13 iPywidgets 1. Characterizing Pigments
- 14 NGLView 1. Characterizing Pigments
- 15 Pigments
- 16 Outline
- 17 Pigment Repairs and Biosymmetry Operations
- 18 Pigment Repairs and Biosymmetry Operations
- 19 Protein Repairs and Mutations
- 20 Protein Repairs and Mutations
- 21 Background and Significance
- 22 Molecular Dynamics MD Organizer
- 23 PyMol and Gromacs Implementation
- 24 Outline
- 25 Structure-Spectrum Connection
- 26 The Frenkel Exciton Model
- 27 Exciton Menu and Spectrum Calculation Window
- 28 Exciton Menu and Spectrum Calculation Window
- 29 Brief Overview and File Organization
- 30 Outline
- 31 Predicting Experimental Electrostatic Frequency Shifts
- 32 Predicting Experimental Electrostatic Frequency Shifts
- 33 Ring Distortion Site Energies with PSI and PSII
- 34 Ring Distortion Site Energies with PSI and PSII
- 35 Site Energy Calculations for Low Symmetry FMO Complex
- 36 Site Energy Calculations for Low Symmetry FMO Complex
- 37 Site Energy Calculations for Low Symmetry FMO Complex
- 38 Site Energy Calculations for Low Symmetry FMO Complex
- 39 Site Energy Calculations for Low Symmetry FMO Complex
- 40 Adjusting Excitonic Parameters with LH2
- 41 Conclusions
