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Spire Tutorial

This simple tutorial will introduce you to the Spire interface, show you how to run SPIDER batch files in Spire, and manage a reconstruction project.

Run spire at the Unix prompt. Put it in background with '&': 
spire &

In Spire's main window, under the Project menu, select New.

This will open the Project edit window. Some of the fields have default values, but you have to supply others. For this tutorial, leave the Project ID blank.

Project title: Specify a title for this project - for this tutorial you can enter "Simple project".

Project file: This file is used by Spire to keep track of a project. PROJECT FILENAME MUST NOT HAVE AN EXTENSION.

Data extension: Specify a file extension for data files - MUST BE 3 CHARACTERS!

Directory for this project: Directory where you will run your SPIDER batch files.

Configuration file: select simple.xml from the drop-down menu.

Create directories and load batch files: Check this box, and click the OK button. Spire will create the project directory, and copy batch files into it, guided by the configuration file.

After loading the configuration for this project, the main window will have several new menus: Dialogs, Batch files, and Sequences.

Under the Dialogs menu, select Test dialog.

This brings up the Test dialog dialog window, which lists 3 SPIDER batch files, mkimg.spi, profile.spi, and stats.spi.

Each batch file may be run by clicking its button.

Each batch file also has an edit button, which lets you see its input and output files. Click the Edit button next to mkimg.spi

A batch file's Edit button opens up the Batch file edit form, which displays the batch file's inputs and outputs.

mkimg.spi is a very simple batch file (click the Editor button to see the actual text of this batch file); it has a single input register and a single output file. You can adjust the image size or change the output filename in this form.

If you made any changes, click Save, then click Execute! to run the batch file.

Spire will run the batch file mkimg.spi in SPIDER. Any output to the screen will appear in Spire's main window:

Spire will report if SPIDER completes successfully, or if there is an error, the last few lines of the results file will be displayed.

Go back to the Test dialog window and run the profile.spi and stats.spi batch files.

Then close the Test dialog window.

Under the Commands menu, select View Project.

The Project Viewer has two sections: completed batch runs are displayed in the upper window, data files are in the lower window. Clicking on a batch run in the upper window displays the output files for that procedure in the lower window. Clicking on a file in the lower window will display that file: images are displayed in Jweb, doc files in a text editor.

If Jweb doesn't start up from the Project Viewer, try to start it in the main window: under the Commands menu, select Open Jweb.