The Settings menu offers the following commands:
| Open | Opens and reads a settings file. |
| Reload | Reloads settings from the current file, which is indicated in this menu item. |
| Save | Saves settings to file. |
| Save As | Saves settings to a new file. |
| Close | Closes settings file to prevent saving to it upon exit. |
| Discard on Exit | Prevents autosaving, saving on exit, and offers to save when reading settings |
| Read Defaults | Reads system default settings file. |
| Autosave | Periodically save settings to currently open file. |
| Set Email Address | Opens dialog box to set address to send emails to. | Set a Property | Changes the value of one program property setting. |
| Basic Mode | Toggles a mode with fewer menu and dialog items displayed if one is defined. |
| Read Basic Mode File | Reads in a new file defining items to hide in Basic Mode. |
| Miscellaneous Options | Options with no other logical place, or not worth putting in a control panel |
| Reverse Wheel Zoom Direction | Sets which direction of mouse wheel movement zooms image up. |
Settings files are used to store just about every parameter that can be set by you in SerialEM. The main exceptions are program states such as Montaging, Low Dose mode, and Tilt Series mode, which need to be activated by you each time you run the program. By default, SerialEM will remember all of your parameters from one session to the next in a file called SerialEMsettings.txt in the directory where SerialEM was started. One can use the options in this menu to save settings into other files and retrieve settings from such files. The menu displays a list of recently used settings files so that you can switch between settings rapidly if necessary. It is also possible to set up a desktop shortcut that makes SerialEM start with a different settings file from the default; see Shortcuts, Command Line Arguments, and Administrator mode.
After parameters are read from a file, that file is left open, which has three implications: 1) Settings can be saved to that file via the entry in this menu; 2) Settings can be restored from the file to the value that they had when they were last saved there; and 3) When you quit the program, settings will be saved into that file. To prevent settings from being saved into a file when you quit the program, just Close the file or use Discard on Exit.
If your settings become too far from usable, you can restore them to default values by reading from a file called the System Default Settings file.
Scripts are not stored in settings files, as of SerialEM 3.8. Instead, they are stored in a separate file referred to as a script package file, and the settings file just has an entry with the name of the script package. When you read a settings file, that script file will also be read and become the current script package file, which will be rewritten when the settings are saved. If you read in a new settings file that loads a different script package, the scripts in the package file will replace the respective ones in the program, but any other scripts that you have defined will be lost (another change in behavior on 12/23/19).
Storing scripts separately makes it possible for multiple settings files to share the same script package, thus preventing diverging versions of the scripts in different files. This will happen as a matter of course when you save a new settings file specialized for some conditions. If you already have multiple settings files from before this change and you want them to share the same script package, first decide which one's package should be the one that is shared. It is recommended that you open that settings file first and use Save Package As in the Scripts menu to save it to a name that indicates its status as the master package. Then open other settings files and use Load New Package in the Scripts menu to load that package.
Use this command to open a file in which settings were stored previously. Ordinarily, your default settings file is open whenever you are running SerialEM. Thus, opening a new file will usually involve closing that file. If this is the case, you will be asked whether you want to save your current settings into the currently open file before closing it and opening a different one.
You will enter the File Open dialog box to select the file, which is a text file.
Below the Open menu entry is a list of the most recently used settings files. Select one of these files to open it. In this case, the settings will automatically be saved to the current file first, without requiring your confirmation. To prevent this, you could close the current settings file first.
Read Again command (Settings menu)
Use this command to read parameter values from the currently open settings file. You would do this if you do not want to keep any parameter changes that you have made and want to restore your settings to the state saved in this file.
Use this command to save settings to a file. If there is a settings file open, then the program state will be saved to this file. If not, you will enter the Save As dialog box to specify a new file to save values into. A file that has been saved into is left open; in other words, it will be saved to again when the program exits, unless you close it first.
Save As command (Settings menu)
Use this command to save settings to a file different from the one that is currently open. You will enter the Save As dialog box to specify a file to save values into. Any previously open settings file will be closed, and the new one will be left open. This means that it will be saved to again when the program exits, unless you close it first. The new settings file will use the same script package file as the old one unless you save the script package to a different name.
Use this command to close a settings file. This means that it will not be saved to when the program exits, which you might want to do if you are going to experiment with parameters that you will not want to save. You will be asked whether you want to save your current settings to the file before closing it.
Discard on Exit command (Settings menu)
This command works like closing the file except that the program will not ask if you want to save settings first, and it will not ask if you want to save settings on exit or when loading new settings. It is useful when settings have reached a state that you do not want saved. It will prevent autosaving as well. The selection will be toggled off again by reading or writing settings, and it does not persist from one run of the program to the next.
Read Defaults command (Settings menu)
Use this command to read the System Defaults settings file. If there is a settings file currently open, you will be asked whether you want to save your settings to that file before overlaying them with the system defaults.
Autosave command (Settings menu)
Use this command to control whether settings will be saved to a file periodically (every 5 minutes, except during a tilt series). Autosaving is useful if you are doing things that present a risk of crashing the program. If no settings file is open when Autosave is on, then nothing will be saved.
Set Email Address command (Settings menu)
Use this command to set the address(es) to which emails from SerialEM will be sent. You can enter more than one address, separated by commas or spaces. The address entered here will be used for any emails sent from SerialEM; i.e., ones sent by the Navigator or a script as well as ones after a tilt series stops.
Set a property command (Settings menu)
Use this command to set the value of one program property. The command can be used with nearly all of the general (non-camera-specific) properties that contain just a single numeric entry and can be set by name in SerialEMproperties.txt. First enter the full name of the property as listed in the properties file or the help file (but matching to this entry is case-insensitive, so case does not matter). If this does not match one of the properties that can be set, an error message is given. Otherwise, another dialog box opens for entering the property value. The existing value of the property is shown in the box.
Basic Mode command (Settings menu)
Use this command to toggle a mode in which selected menu items and dialog elements are not displayed or are disabled. This basic mode must be defined in a file with a list of the desired elements, either a file SEMbasicModeItems.txt in the system directory with the properties file, or a file specified with the property 'BasicModeDisableHideFile'. See Hiding and Disabling Menu and Dialog Items for details.
Read Basic Mode File command (Settings menu)
Use this command to read in a different file defining which items are hidden or disabled in Basic Mode. This filename will be stored in the settings file and reloaded when the program is restarted with those settings, or when those settings are read in.
Reverse Wheel Zoom Direction command (Settings - Miscellaneous Options submenu)
Use this command to toggle whether moving the mouse wheel away from you zooms the image down (the default) or up (the behavior when the option is selected).