CELLmicrocosmos.org - 5. Building a Membrane

Title	Author	Hits
5.6 Manage Title Section	Written by bjoern	Hits: 2280
5.5 3D-Settings	Written by bjoern	Hits: 2430
5.4 More about the 3D Feature	Written by bjoern	Hits: 2337
5.3 Aligning Molecules	Written by bjoern	Hits: 2821
5.2 Dealing with Molecules	Written by bjoern	Hits: 2306
5.1 The File Menu	Written by bjoern	Hits: 2404

Cm2 MembraneEditor
- CELLmicrocosmos project
- Cm1 CellExplorer
- Cm3 CellEditor
- Cm4 PathwayIntegration
- Cm neXt workshop
project ...
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- startCm2 (SSL)
download ...
- downloadCm2 (SSL)
- membrane files
help
- 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
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