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
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.
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.
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.
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
function.
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.
Creates a temporary pdb file of your current membrane that will be opened in Jmol. See Preview your Membrane
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
This optional menu entry is only shown if the path to APL@Voro is set, see 4.2 Web and Local Connections and 9.6 Analysis of PDB Membrane Files with APL@Voro for more information
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
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.
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.