SPIRE

The SPIDER Reconstruction Engine

Installing required packages
--> Troubleshooting and frequently asked questions
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Overview

Spire provides:

A graphical user interface (GUI) for executing SPIDER procedure files and other programs,
A way to manage and organize the many output files created by SPIDER during reconstruction projects.

Spire is designed to simplify running projects that consist of numerous SPIDER procedure files. Users who are new to SPIDER can quickly start processing electron micrographs. Spire provides a convenient environment for testing and debugging procedure files. However, Spire does not deal with program correctness per se - it simply runs your SPIDER procedure files, and saves a list of output files to a project file.

Note: Spire requires SPIDER version 13 or later.

Projects

Spire is organized around projects. Informally, a project typically consists of a set of input electron micrograph images, the procedure files that process this data to produce a reconstructed volume, and various intermediate data files.
A project template is a set of Spider procedure files that carry out a specific technique, such as double-tilt tomographic reconstruction, or reconstruction of single particles with reference projections.
A project consists of applying project template procedure files to actual data files.
Spire project templates are specified by configuration files, which indicate the directory structure of a project and the location of procedure files. The configuration file also specifies how the GUI should present procedure files to the user.
Spire saves information about the current project to a project file, which is a Python "shelve" object. /li>

Dialogs

The graphical interface is organized around dialogs, windows with buttons linked to SPIDER procedure files. Dialogs list a set of conceptually related procedure files, e.g., they may be organized around project subdirectories.

procedure files can be executed in SPIDER by pressing the button with the procedure file's name.

A procedure file can be edited with its accompanying Edit button.

The Help button opens a URL manual page with documentation about the procedure files in this dialog.

The appearance of dialogs is specified by the configuration, and can be changed in the configuration editor.

External database

Although Spire maintains an internal "database" of executed procedure files and their outputs, it may be interfaced to an external project database if your laboratory has one. While the Python coding depends entirely on the details of your local database, an API (Application Program Interface) is provided, along with example code for a MySQL project database. See Using an external database with Spire for details.

SPIDER

You should have a working knowledge of the SPIDER operations that constitute the procedure files you're running. There is plenty of documentation:
Spider home page
A Quick Start Guide to Spider
Spider User's Guide
Spider Manual pages
Reconstruction of Single Particles using Reference Projections (many example procedure files here!)

How to run Spire

At the Unix prompt, type:: spire
or, if you already have a project file, give the project filename as the first argument to Spire (no extension):: spire proj0127
Run it in background mode and you can still use the terminal:: spire proj0127 &

Next: Projects

Updated 22 October 2018

SPIRE

The SPIDER Reconstruction Engine

Table of Contents

Overview