Map fitting

Coot (Emsley and Cowtan, 2004), the crystallographic object-oriented toolkit, is the CCP4 module for model building, model completion, and validation. It is available from the home page of Paul Emsley (www.ysbl.york.ac.uk/ emsley/ coot/). Anyone may download and use the package under the GNU GPL license. A new windows PC version was easily installed. The map fitting tools of Coot version 0.031 were tested. 

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. 

In pleated sheets, we know that successive carbonyl oxygens point in opposite directions. One or two carbonyls whose orientations are clearly revealed by the map can allow sensible guesses as to the positions of others within the same sheet. As mentioned previously with respect to map fitting, we use knowledge of protein structure to infer more than the map shows us. If our inferences are correct, subsequent maps, computed with phases calculated from the model, will show enhanced evidence for the inferred features and will show additional features as well, leading to further improvement of the model. Poor inferences degrade the map, so where electron density conflicts with intuition, we follow the density as closely as possible. 

Proposition 7.4.2 The various signature maps fit together to define a natural transformation of long exact sequences... 

Like the positive reactivity addition case, this transient was run with both the TRACE Brayton performance curves and the CCEP Brayton performance maps. Using the CCEP Brayton performance map fit option produced the most severe transient and is shown in the attached figures. Results are also shown with and without an automatic reactor temperature control system. The results with and without active Tava control are provided below. 

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