Finding and analyzing difference map peaks
- Overview
- Configuration
- Output
Overview
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.
Configuration
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.
Output
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.
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