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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Alex,
<div>You can probably use phenix.find_peaks_holes to do step #3:</div>
<div><br>
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<div>
<p class="p1"><span class="s1"> Prints a summary of all peaks and holes above the specified cutoff in the</span></p>
<p class="p1"><span class="s1"> mFo-DFc map, and flag any water molecules with suspiciously high peaks</span></p>
<p class="p1"><span class="s1"> (possible ions). Will also check the anomalous map if available.</span></p>
<p class="p1"><span class="s1"><br>
</span></p>
<p class="p1"><span class="s1">All the best,</span></p>
<p class="p1"><span class="s1">Tom T</span></p>
<p class="p1"><span class="s1"><br>
</span></p>
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<div id="divRpF387167" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Alejandro Virrueta [alejandro.virrueta@yale.edu]<br>
<b>Sent:</b> Wednesday, April 15, 2015 7:54 PM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] find difference peaks<br>
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<div dir="ltr">Hello,
<div><br>
</div>
<div>I'm working on a small project, and need some feedback.</div>
<div>I am trying to rebuild methionine side-chains by looking at the difference peaks for a given Fo-Fc map.</div>
<div>I envision a process as follows:</div>
<div><br>
</div>
<div>1. Delete the MET side-chain of a PDB file</div>
<div>2. Refine structure to get Fo-Fc map</div>
<div>3. Get a list of the peak positions relative to the coordinates of the PDB file I used</div>
<div>4. Filter list by keeping peaks near the MET C alpha/beta PDB coordinate.</div>
<div>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)</div>
<div><br>
</div>
<div>What functions should I use to achieve step 3?</div>
<div>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')?</div>
<div><br>
</div>
<div>I hope this makes some sense to someone.</div>
<div><br>
</div>
<div>Thanks!</div>
<div>Alex</div>
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