To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction (MAD) and multiple isomorphous replacement (MIR) phasing can be powerful tools to obtain low-resolution initial phases from heavy-atom derivative datasets, then phase extension is needed against high-resolution data to obtain accurate struc-tures. In this context, we propose a direct-methods procedure here that could improve the initial low-resolution MAD/MIR phase quality. And accordingly, an automated process for extending initial phases to high resolution is also described. These two procedures are both implanted in the newly released IPCAS pipeline. Three cases are used to perform the test, include-ing one set of 4.17 ? MAD data from a membrane protein and two sets of MAD/MIR data with derivatives truncated down to 6.80 ? and 6.90 ?, respectively. All the results have shown that the initial phases generated from the direct-methods procedure are better than that from the conventional MAD/MIR methods. The automated phase extensions for the latter two cases starting from 6.80 ? to 3.00 ? and 6.90 ? to 2.80 ? are proved to be successful, leading to complete models. This may provide convenient and reliable tools for phase improvement and phase extension in difficult low-resolution tasks.