[phenixbb] find difference peaks

Alejandro Virrueta alejandro.virrueta at yale.edu
Wed Apr 15 18:54:32 PDT 2015


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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150415/68da1358/attachment.htm>

More information about the phenixbb mailing list