New phases from the molecular model

The Fo Fc map emphasizes errors in the current model, but it lacks the familiar appearance of the molecular surface found in an FQ map. In addition, if the model still contains many errors, the F — Fc map is noisy, full of small positive and negative peaks that are difficult to interpret. The FQ— Fc map is most useful near the end of the structure determination, when most of the model errors have been eliminated. The FQ— Fc map is a great aid in detecting subtle errors after most of the serious errors are corrected. 

A more easily interpreted and intuitively satisfying difference map, but one that still allows undue influence by the model to be detected, is the 2FQ — Fc map, calculated as follows 

As the model is built, the viewer sees the model within the map, as shown in Plate 2 b. As the model is constructed or adjusted, the program stores current atom locations in the form of three-dimensional coordinates. The crystallogra-pher, while building a model interactively on the computer screen, is actually building a list of atoms, each with a set of coordinates (x,y,z) to specify its location. Coordinates are automatically updated whenever the model is adjusted. This list of coordinates is the output file from the map-fitting program and the input file for calculation of new structure factors. When the model is correct and complete, this file becomes the means by which the model is shared with the community of scientists who study proteins (see Section VII). 

Following is a somewhat idealized description of how map fitting may proceed, illustrated with views from a modern map-fitting program. The maps and models are from the structure determination of adipocyte lipid binding protein (ALBP), which I will discuss further in Chapter 8. 

When the map has been improved to the point that molecular features are revealed, the crystallographer attempts to trace the protein through as much 

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