Finding and analyzing difference map peaks



phenix.find_peaks_holes is a utility for identifying points of interest in difference maps, typically at the end of refinement. It will calculate an mFo-DFc map and locate peaks and holes, plus anomalous map peaks (if anomalous data are provided) and flagging of waters with suspiciously high mFo-DFc values. This information may be used to improve the model, especially in the addition of solvent and small ions.


The program requires only a PDB file and data (including R-free flags). The default options should be sufficient for most cases, although for very large structures or especially noisy maps, you may find it helpful to increase the sigma cutoff.


By default, peaks which overlap with the input atoms (within a cutoff distance) will not be included. If you want to find all peaks, set the minimum peak-model distance to zero. Additional options are available by clicking the "Peak search" button.

On the command line, the minimal input is simply the paths to your model and data files (column labels may need to be specified if the choice is ambiguous). Running the program without arguments will print out a summary of available options, which are also listed below.



A summary tab will appear at the end of the run with peak counts, plus output files and buttons to view them. By default the program will write a PDB file containing up to five "chains", all with atoms labeled UNK:

  • A: mFo-DFc peaks (positive).
  • B: mFo-DFc holes (negative)
  • C: anomalous map peaks
  • D: waters in mFo-DFc peaks
  • E: waters in anomalous peaks

The program will also write the 2mFo-DFc, mFo-DFc, and anomalous (if available) maps. Additional tabs will display each type of result in a list; clicking these items will recenter the view in Coot and/or PyMOL on the selected point.

List of all available keywords