5.1 The File Menu
The menu 'File' is the first menu in the program's menu bar. It contains items for most of the basic operations that you will need while working with the editor. Most items can also be accessed from the toolbar or by using the specific key shortcuts.
The 'File' menu
The 'File' menu provides the following options:
New Membrane Model
Opens a dialog for creating a new membrane.
This dialog prompts you to enter the following values:
|Header||The classification string located in the first line of a pdb file|
|Code||The pdb id string located in the first line of a pdb file|
|Size||The initial X/Z bounds of the membrane in angstrom|
Note that these values are just initials and that they may be edited at any time.
Press 'Create' in order to activate the new membrane. If a previous membrane was already open, then it will be discarded at this point.
Load Membrane Model
Opens a file chooser that lets you choose and open an existing membrane. You are only able to select valid membrane files that were created by this application. Those are indicated by a specific membrane icon . Press 'Open' to load your selected membrane.
Rebuild Membrane Model from PDB FileOpens a filechooser that allows you to select an existing membrane in pdb format in order to reimport it. See how to rebuild an existing membrane model
Save Membrane Model As...
Opens a filechooser to save your current membrane. You can select an existing membrane file or you can create a new one by entering a new name. Press 'Save' and the membrane will be written into the selected file.
Save Membrane Model (Quicksave)
Saves your current membrane to its associated file. If your membrane is new and no file has been determined for it, you will then be prompted to choose one. Otherwise, this works as a quicksave
Save Membrane Image Model As...
Opens a filechooser to save your current image of the membrane. A screenshot is taken from the actual MembraneView, including the regular membrane, the protein alignment mode and the lipid default alignment mode. You can select an existing image file or you can create a new one by entering a new name. Press 'Save' and the membrane will be written into the selected file.
If you need the image for a publication, please keep in mind that the MembraneEditor uses Java3D, which in turn usually uses OpenGL. So if you tune the OpenGL settings of your graphic card, this will normally also affect the rendering quality of the membrane. For example it is normally possible to increase the AntiAliasing settings of your graphic card, which negatively affects performance, but improves the image quality drastically.
In addition you can use the options of the MembraneEditors' 3D Settings to change a lot of details. For example you may prefer a uniform background. In this case you can just activate this setting in the Appearance dialog of the 3D Settings.
Preview Membrane in Jmol
Creates a temporary pdb file of your current membrane that will be opened in Jmol. See Preview your Membrane
Preview Membrane as Pdb File
Creates a temporary pdb file of your current membrane that will be opened for textual previewing in the Pdb-File-Browser. See Preview your Membrane
Generate the Pdb File
Opens a dialog where you can save your membrane as a pdb file. See Generating and Options
Opens the manager that allows you to edit the title section of your membrane. See how to manage the title sections
Opens a dialog where you can redefine your membrane bounds. If you choose a larger size than before, the membrane space will simply be extended. If you choose a smaller size, then all molecules located
outside the new range will be removed from your membrane.
Switches to a mode where you can define and activate a new micro domain. See how to use microdomains
Add Secondary Bilayer
Opens a dialog to create another bilayer in the model. See how to use multilayers
Reloads all molecules inside your current membrane (including the sample lipids in the Component View).
This is necessary if you want to apply your detail settings to all members instantly, or if a pdb file has been changed somehow during the runtime of the Membrane Editor.
Using the Quickload Items
There are up to 4 quickload items located in the lower part of the menu. Use them to open one of your previously used membranes.
Saves your current settings and closes the MembraneEditor. You will be prompted for this in case your current membrane contains unsaved changes.
- Written by bjoern
- Category: Cm2help 5. Building a Membrane
- Published: 14 September 2013
- Hits: 2111