The Options panel in Spire


The Options panel is found under the Commands menu.


User preferences are saved to an external file, usually .spire, in the user's home directory. This file is read whenever Spire is started.

Preferences menu
numerous preferences that are toggled on/off.
Click the large purple "Preferences menu" button to view these.

Balloon help : turn on/off floating help messages

save output files to project file : if turned off, Spire will not scan the results files for output files. The project file will consist of a list of executed Procedure files, without any of their outputs.

save results file : save/delete results file REGARDLESS OF LAST LINE IN Procedure FILE

save log file : save messages to Spire's main window into a text file

ask before deleting : always prompt the user before deleting a file

check for prior runs : see if executing a Procedure file will overwrite any outputs.

use filenums entry : if checked, the "File numbers" entry box in Spire's main window takes precedence over a file numbers doc file.

Start Jweb at startup : try to start up a copy of Jweb when Spire starts up. Spire will then use use Jweb to display images.

Other Preferences

no. of lines to show in results file : for the "check progress" button in Spire's process window.

display program for images : Jweb by default, but can be any image display program that accepts an image filename on the command line, such as image.gif. (Must accept SPIDER image format).

max no. of files to display : when viewing outputs of a selected Procedure run.

editor : text editor linked to "Editor" button, at the bottom of a Procedure file form. You may select from the drop-down list, or type in your own preference.

Execution environment : select the machine where Spider commands are to be executed.

Save : save preferences to the Spire user preference file,

Reset : reset preferences to values in the Spire user preference file.

Defaults : reset preferences to system default values.


Font types and sizes can be changed in this interface.

Small font is used to view the tables of Procedure runs and output files.

Main font is used by most windows, menus, buttons, etc.

Large font is used by large labels, usually window titles.

Output font is used in Spire's main output window, to display output messages from Spider.


The System panel shows the values for numerous system parameters.

threshold for large directories : when traversing directories, Spire will not list the files if the directory size exceeds a limit, as measured by the stat command.

file numbers file : the file numbering doc file to create, when saving numbers from the File Numbers entry box.

parameter file : the doc file to create when saving project-wide parameters.

configuration file : the default xml configuration file.

Help URL : A URL to be loaded into a browser when the user hits the 'Help' button. It should describe the project Procedure files.

SPIDER command : the name of the command to run SPIDER on this system

Main label text : Text in the main window for all related projects

image file : image logo in main window. It should be a gif image about 100 x 100 pixels.


Used mainly for debugging, this panel displays the values of various Python objects. This will probably only make sense if you know some Python. There are two Python modules (source files) used for holding numerous global variables, and (the latter is for graphical variables).

view project : displays the value of the object GB.P, which encapsulates the state of the current project.

view GB : displays the value of the object GB, which holds various global variables (see the Python source file

view preferences : displays the value of the object GG.prefs, which holds various user preferences.

View it : an entry for evaluating arbitrary Python objects, e.g., GG.sysprefs.