Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
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 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 standard method of calculating such an envelope follows the algorithm proposed by B.-C. Wang (Meth. Enzym., 115, 90-112 (1985)) which uses a weighted average of the electron density map. 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 of the molecule. We have 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 ~60% of the molecule, led to little improvement in the map interpretability. However, a significant improvement of the map could be achieved when a better envelope was used in the procedure. We evaluated various methods of calculating the molecular envelope and investigated the effect of the shape of the envelope on the modified electron density map. Based on these computational experiments we propose an improved procedure to calculate the envelope from a partial molecular replacement model, where the calculations of the envelopes for the known and unknown parts are performed in separate steps.