New routine for thinning, editing and fitting MIR maps using real-space molecular dynamics

A new routine has been developed for fitting multiple isomorphous replacement (MIR) maps. The map is first thinned and reduced to a series of 'traces'. Each trace consists of a main trace of defined length and a series of branching side traces. Using this trace representation, the entire map can be viewed at one time and the major secondary structural features can be recognized. A number of features have been built into the routine for editing these traces, allowing neighboring traces to be connected and incorrect connections to be broken. After the traces have been edited, a polyserine fit is generated. The traces are used to guide the initial positioning of a short polyserine segment. This segment is then refined using a real-space molecular-dynamics procedure, which uses the gradient of the electron density as a pseudoforce on the polyserine atoms. After the structure of this initial polyserine has been refined, another serine is added at one end, a short period (about 10 s on a personal Silicon Graphics IRIS workstation) of molecular dynamics is applied and the procedure is repeated. The final refined structure depends only on the electron density and is independent of the thinned traces. The routine is illustrated with two examples. One example uses the 3.0 angstrom map generated directly from a model protein. This allows direct comparison between the polyserine fit and the model that was used to generate the map. The second example uses the experimental MIR map for lipovitellin. This is a very large protein (about 1300 amino acids), which has a poor-quality map that has not yet been refined. The program makes extensive use of Silicon Graphics graphical (GL) routines.