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<div class="moz-cite-prefix">Hi,<br>
<br>
what kind of file you use to see the map in Coot: Fourier map
coefficients (MTZ file) or actual map (CCP4 binary formatted file
with the map)? I need to know this before offering a first guess
on what may be the reason for this.<br>
<br>
Pavel<br>
<br>
On 1/13/13 11:38 AM, CPMAS Chen wrote:<br>
</div>
<blockquote
cite="mid:CAAU4GKafXqGesovngWD3Esfhp_Aj7RfUOL7xsdntrZmkFvNuVg@mail.gmail.com"
type="cite">Dear PhenixBBer,
<div><br>
</div>
<div>I recently updated my old phenix-1.6.4-486 to
phenix-dev-1266. To my surprise, the absolute electron density
on the 2Fo-Fc map is quite different.</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png">https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png</a></div>
<div><br>
</div>
<div>At the same sigma level(1.5), the absolute density of the
violet map is 0.32e/A^3 (phenix-dev-1266), while that of the
blue map is 0.01e/A^3(phenix-1.6.4-486). Besides the different
phenix used, there is no other difference on the data and model
used.</div>
<div><br>
</div>
<div>Sam encountered a similar problem on the density. </div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html">http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html</a> </div>
<div><br>
</div>
<div>By the way, is there a simple way to keep only F and SIGF
column of the autoxds generated truncate.mtz via phenix? the GUI
does not allow to reduce columns. I normally use IMEAN and
SIGIMEAN to do refinement, but this may not be necessary as it
is pointed in the maillist, since the intensity is already
transformed to amplitude after truncation in autoxds.</div>
<div><br>
</div>
<div>I can specify labels by xray_data.labels = "F, SIGF", but
apparently phenix treats it as containing anomalous data. the
following is extracted from the refine pdb file</div>
<div><br>
</div>
<div>
MIN(FOBS/SIGMA_FOBS) : 1.16 </div>
<div>REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 </div>
<div>REMARK 3 NUMBER OF REFLECTIONS : 143207 </div>
<div>REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247</div>
<div><br>
</div>
<div>Also, in the auto generated def file, </div>
<div>xray_data.labels = "F, SIGF, DANO, SIGDANO"</div>
<div><br>
</div>
<div>Or there is a work round for this issue?</div>
<div><br>
</div>
<div>Thanks! <br clear="all">
<div><br>
</div>
-- <br>
<p>***************************************************</p>
<p>Charles Chen</p>
<p>Research Associate</p>
<p>University of Pittsburgh School of Medicine</p>
<p>Department of Anesthesiology</p>
<p>******************************************************</p>
</div>
<br>
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<br>
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</pre>
</blockquote>
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