Software Tools For Molecular Microscopy

There are a large number of software tools or software applications that have been specifically developed for the field sometimes referred to as molecular microscopy or cryo-electron microscopy or cryoEM. Several special issues of the Journal of Structural Biology (see references below) have been specifically devoted to descriptions of these applications and several web sites provide partial lists of the software packages and where to obtain them. This article attempts to provide a complete list and up-to-date distribution information of all of the software of interest to the cryoEM community. Everyone in the community is encouraged to add content, correct errors, and make any other contributions that might be useful.


The software tools described here have been loosely and somewhat arbitrarily organized into several categories as follows:

  • General packages: Packages that offer a comprehensive set of tools to permit the analysis of data in several classes of structural problems.
  • Specific packages: Packages that offer a comprehensive set of tools to permit the analysis of data in a single class of structural problem. For example packages specifically focused on objects with helical, icosahedral, crystalline symmetry, etc.
  • Application tools: Packages that offer a tool or a set of tools to permit the analysis of data in one or more class of structural problems. These have generally been developed to manage one specific step in the structural analysis, for example CTF correction, particle picking etc.
  • Utilities: General utilities like file format conversion, difference mapping, etc.

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Last modified on 19 July 2012, at 09:17