Procedure to calculate the molecular envelope from a partial model

Density-modification algorithms have gained, in recent years, a widespread use in the early stages of protein structure determination, especially in combination with the single isomorphous replacement, the multiple isomorphous replacement and the multiple-wavelength anomalous dispersion methods, where density modification usually leads to a significant improvement in the quality and interpretability of the initial electron-density map. The current computer programs which are used to perform this task combine several approaches, an important component of which is the solvent-flattening procedure. The latter procedure depends crucially on the correct determination of the molecular envelope. The solvent-flattening procedure has also been applied to the electron-density maps calculated from partial models obtained from the molecular replacement method. In such case the envelope calculated in the standard way does not always encompass entirely the missing part. It has been found that the standard application of the density-modification method (as implemented by programs SQUASH and DM) to a map calculated from a molecular replacement model containing similar to 60% of the molecule, led to little improvement in the map interpretability. Here, it is shown that a significant improvement of the map can be achieved when a better envelope is used in the procedure. Various methods of calculating the molecular envelope have been evaluated, the effect of the shape of the envelope on the modified electron-density map has been investigated and an improved procedure to calculate the envelope from a partial molecular replacement model is proposed.