coordinates: the 3-dim coordinates present in the file are stored into

the neuron definition file. This option has no advantages in Nodus 3.1, it reduces the maximum number of compartments from 4000 to 3000.

Automatic compartment names: compartment names are generated automatically. These

names reflect morphological information, like branching order. Do not use this option if the

Select only named comparts option in the Preferences dialog is set, because all

Close ‘a window’

Is enabled if any window is displayed.

If it is a definition window, its contents are checked and stored in memory if no errors were found. If any parameter value in the window is not acceptable, Nodus will alert the user and the window will not be closed.

If the contents of the window were changed and these changes were not Saved, Nodus will alert the user before closing the window (if the appropriate Warnings option is active in the

Preferences dialog).

Figure V/9: Warning shown before a window is Closed that has been edited, but not

Saved. Press Yes to save the changes and close the window; No to close it

without saving; if Cancel is pressed the window is not closed and not saved.

The action of the Close command depends on whether the window belongs to a linked file or not. If it is a file linked to other files in memory (see the ‘Nodus Files’ section in chapter IV for more details), the window will be hidden. Otherwise the window will be closed and all its data will be removed from memory.

Hide ‘a window’

This command is available when the shift key is pressed and if any window is displayed.

If it is a definition window, its contents are checked and stored in memory if no errors were found. If any parameter value in the window is not acceptable, Nodus will alert the user and the window will not be hidden.

The window data remain in memory after the window is hidden. The window can be displayed again by selecting the menu item with the same title at the bottom of the appropriate menu.

Kill ‘a window’

The command is available when the shift and the option key are pressed while a window is present.

Kills the window, i.e. the window is closed without checking it contents. Any changes made to the window contents are not stored. This command is useful to quickly close a window that has several bad parameter values in it.

Close All

Is enabled if any window is displayed.

Closes all Nodus windows in the same way as consecutive Close ‘a window’ commands. Refer to Close ‘a window’ for more details.

Hide All

This command is available when the shift key is pressed and if any window is displayed.

Hides all Nodus windows in the same way as consecutive Hide ‘a window’ commands. Refer to Hide ‘a window’ for more details.

Close All Graphs

This command is available when the option key is pressed and if any window is displayed. Closes all graphic windows, i.e. old simulation plots (not the active Plot Window), Neuron Diagrams and Conductance Plots. There is no option to save these windows first.

Save ‘a window’

Is enabled if any definition or simulation window is displayed.

The window contents are checked and stored in memory if no errors were found. If any para- meter value in the window is not acceptable, Nodus will alert the user and nothing will be saved. The contents of the corresponding definition file are updated. The name and hidden ID-number are not changed (see Fig. IV/6). If the file has never been Saved before (still called ‘Untitled’) the Save As dialog (Fig. V/10) is presented.

Save As…

Is enabled if any definition or simulation window is displayed.

Figure V/10: the Save As file dialog window for conductance (left) and neuron (center)

definition files. At right the File format popup menu.

Presents the standard minifinder dialog window which lets the user supply a new name and/or folder location for the file. Press Save to confirm the command. A new file will be created; it will have the new name and a new hidden ID-number. The old file is not changed.

Options:

Update all links in memory: all links in hierarchically higher files in memory that point to

this file are updated to link to the new file instead of the old file. See the ‘Nodus Files’ section in chapter IV and Fig. IV/6 for more details.

File format (neuron definition files only): neurons can either be saved in the Standard

Nodus format (default, this is the only format that can be Opened) or some of the data can be written to a text file. A text file can be either an Import Neuron File Format (Ladder or

Genesis, see the ‘Appendix’) or it can be similar to printed output (Text). Page Setup …

Presents the standard Macintosh® page setup dialog, specific for the active printer. Use this command to specify the page size and any reduction or enlargement. The settings are kept in memory till Nodus quits. The 50% Reduction option is very useful if the Double size

simulation plots option in the Preferences dialog is selected. Print…

Is enabled if any definition or graphics window is displayed.

The standard Macintosh® print dialog, specific for the active printer, is presented so that the user can select the number of copies, the quality of printing, etc. The contents of the window are printed, the date and the window title are printed in a header. If it is a graphics window the graphic is printed as it is displayed. Do not use draft printing for graphics! If it is a definition window the complete definition is printed, using the Print font specified in the Preferences dialog. Note that printing of large neuron definition files may take a lot of time. No dialog is shown during the preparation or the actual printing. Actual printing can be interrupted by pressing command-period.

Automatic Saving

The Automatic Saving feature makes Nodus save the simulation database with all integration, output and experiment settings and the simulation results (including the Plot Window) in the

Nodus Resume file on Quitting. When Nodus is restarted, the application will look for this file

and load all data so that Nodus behaves as if it had never been interrupted. An instruction window is displayed if a simulation database present:

Figure V/11: the Automatic Saving instruction window.

This command is a toggle: a check mark is shown when the automatic loading/saving feature is on, select the command again to turn it off.

The automatic command saves only the simulation database, definition files are not saved auto- matically (but the appropriate warnings will be displayed before Quitting).

Quit

When this command is selected Nodus closes all windows and output files, writes a Nodus

Resume file if the Automatic Saving command is on, and returns to the Finder.

Nodus will check whether all definitions and the simulation database have been saved correctly if the appropriate Warnings option is active in the Preferences dialog. An alert will warn the user if any data have not been saved correctly, see Fig. V/8 (the Cancel button interrupts the

Quit command).