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7.3. Changing Granularity / Coarse Graining
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Cm2 MembraneEditor
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1. Introduction ...
1.1. About the MembraneEditor
1.2 Features
1.3 The UI Components
1.4 Requirements
2. The GUI ...
2.1 Using the GUI
2.2 Shortcuts
2.3 3D Stereoscopy
3. Managing local PDB Files ...
3.1 Setting a Database
3.2 Handling your files
3.3 Gaining Information
3.4 Managing Models
4. The PDB Integration ...
4.1 Search & Download
4.2 Internet Configuration
5. Building a Membrane ...
5.1 The File Menu
5.2 Dealing with Molecules
5.3 Aligning Molecules
5.4 More about the 3D Feature
5.5 3D-Settings
5.6 Manage Title Section
6. Special Membrane Properties ...
6.1. Using Microdomains
6.2. Using Multilayers
7. Atomic Representation
7.1. About
7.2. Predefine Conformation
7.3. Changing Granularity / Coarse Graining
8. The Lipid Bilayer ...
8.1 Running a Membrane Algorithm
8.2 Included Algorithms
8.2.1 Linear Placing
8.2.2 Random Placing
8.2.3 Advanced Random Placing
8.2.4 Simulated Annealing
8.2.5 Distributor
8.2.6 Atom Level Minimizer
8.2.7 The Wanderer (Rookie)
9. Generating Output ...
9.1 Pdb output settings - Dealing with limitation and compatibility issues
9.2 Written Contents
9.3 Preview your Membrane
9.4 Saving the Membrane File
9.5 Rebuild Membrane Model from existing pdb file
9.6 Membrane Analysis with APL@Voro
10. Import / Manage Algorithms
11. More about the Editor ...
11.1 Future Plans / Known Issues
11.2 Cm2 Team
11.3 Copyright
11.4 List of external Sources and Packages
11.5 History
developer ...
Introduction
Library and Documentation
Creating a new Membrane Algorithm
Overriding the Methods from the interface
Essential Methods and Objects
Finishing your Membrane Packing Algorithm
Writing a good Membrane Algorithm
Example
Forcefield Development Hints
videos
publications
apl@voro ...
about
algorithms
screenshots & videos
forum