Hi Alex, You can probably use phenix.find_peaks_holes to do step #3: Prints a summary of all peaks and holes above the specified cutoff in the mFo-DFc map, and flag any water molecules with suspiciously high peaks (possible ions). Will also check the anomalous map if available. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Alejandro Virrueta [[email protected]] Sent: Wednesday, April 15, 2015 7:54 PM To: [email protected] Subject: [phenixbb] find difference peaks Hello, I'm working on a small project, and need some feedback. I am trying to rebuild methionine side-chains by looking at the difference peaks for a given Fo-Fc map. I envision a process as follows: 1. Delete the MET side-chain of a PDB file 2. Refine structure to get Fo-Fc map 3. Get a list of the peak positions relative to the coordinates of the PDB file I used 4. Filter list by keeping peaks near the MET C alpha/beta PDB coordinate. 5. Try to rebuild side-chain after anchoring the sulfur atom (assuming sulfur is located at the highest peak and within some distance to C beta) What functions should I use to achieve step 3? I am also trying to implement this process within the ringer program (phenix/cctbx_project/mmtbx/command_line/ringer.py). If anyone is familiar with this, what commands would work best within this ringer program? i.e. what functions can operate on difference_map (which is sampled by a point using tricubic_interpolation under 'def sample_angle')? I hope this makes some sense to someone. Thanks! Alex