Spire Projects
Starting a new project
Opening an old project
Edit: changing the attributes of a project
The project file
Informally, a project refers to processing a particular set of data to produce a reconstructed volume.
Spire saves information about the current project to a project file, which is a Python "shelve" object.
A project in Spire consists of:
- input files,
- e.g., micrographs, a reference volume, noise template, etc.
- a set of batch programs,
- e.g., the batch files for Single
Particle Reconstruction, and other techniques
- a configuration file, which specifies:
- directory structure & location of batch files,
- organization of the GUI into dialogs,
- the project file itself.
After several batch files have been run and their outputs
saved, a project also contains
- a run list of all successfully executed batch files,
- a set of output files associated with each batch "run"
Starting a new project in Spire
Under the Project menu, select New. This opens the Project window.
If you are using an external project database, the Project ID is the key number for this project in the database. If the project database already has some information about the project, Spire will attempt to fetch this information.
NB: changes made to Spire project will not automatically transfer to the external project database. Spire can only make such changes with the upload utility.
If you are not using a project database, leave the Project ID blank.
The project form pops up with the following entries (some of these may have been obtained from the external database):
- Project title
- Enter a brief descriptive title of this project.
- Project file
- A filename to store project information. E.g., if the Project ID is 123, you can call this file proj123
The project file must NOT have an extension!
After this, you can start up Spire with the command
spire proj123
- Data extension
- The Spider data extension (3 characters).
- Host machine
- The name of the computer you wish to execute the Spider program.
If the project host machine is not the same as the computer the user is currently logged into, Spire will execute Spider commands remotely.
- Directory for project
- The working directory for the project, hereafter called the project directory. You can use the Browse button to select a directory.
By default, Spire will suggest a 3-letter directory named after the project data extension.
- Configuration file
- An XML file that specifies the source batch files, the directory structure, and some graphical interface information for this project. See config.html for details.
- Create directories and load batch files
- You should always check this if you're starting a new project, and intend to run anything.
When you click "OK", Spire
- creates the project directory and subdirectories,
- copies batch files from the source directory to the project directory,
- creates the project file in the project directory, and makes a local copy of the configuration file,
- creates additional menus in the top menu bar, Dialogs and Batch files,
- opens up a form for Project Parameters.
Opening an old project
Start up spire with the project file on the command-line:
spire project_file
Or, under the Project menu, select Open, and select the project file.
Editing a project
Under the Project menu, select Edit, and make the desired changes to the project file.
You can reload a new set of batch files by checking the "Create directories and load batch files" box.
NB: changes made to Spire project will not automatically transfer to the external project database. Spire can only make such changes when explicitly requested with the upload utility.
The project file
To view the current state of the project, under Commands menu, select View project. A table lists the Spider batch files that have been run for this project. The output files for each batch file can also be viewed.
Spire saves information about the current project to a project file, which is a Python "shelf" object. It is not a text file, and its internal workings are handled by Spire. If absolutely necessary, its contents can be explored: under Commands menu, select Options, then choose the Inspect tab. Once loaded, the project file is referred to as "GB.DB". Type "GB.DB" in the entry and click "View it".
