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The X-ray Crystallographic Module

This module calculates the function value, gradient, and curvature for the term of the function that involves the crystallographic data. This term is

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Because of the number of reflections in the average protein structure and the amount of time it takes to calculate them from a structural model, this module uses the largest portion of CPU time of the entire refinement cycle.

In a long loop this module must be able to calculate the function value, gradient, and curvature of the function. To calculate any of these quantities structure factors must be calculated from the current model and scaled to the observed structure factors. Once this is done the function value and curvature can be directly calculated. The gradient is calculated via the method of Agarwal which requires that a difference map be convoluted with a separate function for each parameter in the model. The program Rfactor performs all these tasks.

In the long loop both the term's value and gradient must be calculated while in a short loop only the term's value is required. The curvature will be required if the gradient/curvature or preconditioned conjugate gradient methods of refinement are to be used.





Dale Edwin Tronrud
Thu Jul 6 23:24:57 PDT 2000