[phenixbb] find difference peaks

Terwilliger, Thomas Charles terwilliger at lanl.gov
Wed Apr 15 19:59:51 PDT 2015

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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Alejandro Virrueta [alejandro.virrueta at yale.edu]
Sent: Wednesday, April 15, 2015 7:54 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] find difference peaks


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.

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