===== Structure determination from electron micrographs of two-dimensional crystals =====
**By Vinzenz Unger and Anchi Cheng**

The following section provides a general description how to analyze (low-dose) electron micrographs of two-dimensional crystals. In summary the whole procedure can be divided into 5 steps:


  * **Step 1:**[[Stepone|Optical diffraction, image acquisition and preparation, determination of lattice parameters, calculation of unit cell dimensions and magnification, calculation of a filtered image.]]
  * **Step 2:**[[Steptwo| Correction of lattice distortions, extraction of raw image data and correction of phases for the effect of the contrast transfer function (CTF).]]
  * **Step 3:**[[Stepthree| Determination of plane group symmetry.]]
  * **Step 4:**[[Stepfour|Combination of data from different images, data refinement, data averaging and generation of projection density maps.]]
  * **Step 5:**[[Stepfive|Determination of tilt geometries.]]
  * **Step 6:**[[Stepsix|Merging of 3D data, lattice line fitting, data refinement and calculation of 3D density maps.]]


A number of examples are given to explain the effect of certain procedures and to illustrate the impact of inaccurately determined image parameter. All examples are taken from a study investigating the structure of a recombinant gap junction channel. The larger thickness (>150Å) of this specimen causes some of the illustrated effects to be very pronounced. If a thin specimen (~ 80Å thick) is analyzed some of these effects are more subtle yet it seemed more reasonable to give examples that are easy to understand.

Following this general account is a more detailed description of the current MRC program package that also provides some more in depth information about how to optimize the processing steps. Finally, a number of explicit protocols can be found at the end of this chapter. The protocols cover only the basic routines due to space limitations.