Getting Started with SPIDER

SPIDER provides a large Manual of Operations, each of which is documented in a separate manual page. Nobody likes to read manuals. On the other hand, this is the only way to make sure that the computer performs the operation you are intending.

A good way to start from scratch is the Quick Start Guide. The Tutorial provides a more detailed survey of the many image and volume processing operations in SPIDER. In general, if you run into terms that you don't know, try the Glossary. It provides simple explanations that may be sufficient for the time being. If you want to get into more detail, there is a number listed for each term in the glossary, referring to the page of the book: J. Frank Three-Dimensional Electron Microscopy of Macromolecular Assemblies Oxford University Press, (February 2006)

After going through the tutorial, you should look at the formal description of the formats, rules and syntax, provided in the User's Guide. This is a document that you will have to go back to frequently as you get more familiar with the SPIDER environment, especially if you want to use the language to the fullest extent, including nested procedures, do-loops, registers and document files.

Next, you may want to look under "3D Techniques". This part of the documentation goes into the detailed procedures that are used to accomplish a 3D reconstruction. Even if you are not interested in any particular approach, the procedure files performing the individual tasks, such as density normalization and alignment, will show you how operations are used in context.

When you are getting started, the alphabetic listing of operations might not be especially useful, because you don't know the idiosyncratic names under which they can be found. We therefore have provided a cross reference index that helps you identify the relevant operations from an alphabetic listing.


Source file: starting.html     Updated: 12 Jun. 2012     Author: Joachim Frank
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