That could be right. Would you suggest to do the averaging in CCP4 instead?<br><br>Ursula<br><br><div class="gmail_quote">On Mon, Dec 12, 2011 at 11:35 AM, Tom Terwilliger <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Hi Ursula,<div><br></div><div>I am not sure if this is the (only) problem, but phenix.ncs_average does not know about NCS groups, so it only takes the first NCS group and averages it and writes out the map where that group has been averaged.�</div>
<div><br></div><div>So supposedly phenix.ncs_average should (1) average the density in the region where the 1st NCS group applies, and (2) leave original density elsewhere.</div><div><br></div><div><div>Is that consistent with what you see?</div>
</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br><div><div><div class="h5"><div>On Dec 12, 2011, at 12:27 PM, Ursula Schulze-Gahmen wrote:</div><br></div></div><blockquote type="cite"><div>
<div class="h5">I am puzzled about my ncs-averaged output map. <br>I determined the ncs relation using phenix.find_ncs with pdb and mtz input. The program finds 2 NCS groups with 3 molecules each and the rmsds are low. I then read in the ncs_spec file and an mtz file with map coefficients into phenix.ncs_average. I used the FOFCWT, PHFOFCWT coefficients. The output map seems cleaner than the unaveraged map and shows some of the same features, but the density around the 3 molecules is not identical. 2 of them look very similar, but the density around one of them is somewhat different. How is this possible if the map is averaged?<br>
<br>Thanks for any suggestions or explanations.<br><br>Ursula<br><br><br clear="all"><br>-- <br>Ursula Schulze-Gahmen, Ph.D.<br>Assistant Researcher<br>UC Berkeley, QB3<br>356 Stanley Hall #3220<br>Berkeley, CA 94720-3220<br>
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<div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel:� <a href="tel:505-667-0072" value="+15056670072" target="_blank">505-667-0072</a>���������������� email: <a href="mailto:terwilliger@LANL.gov" target="_blank">terwilliger@LANL.gov</a><br>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Ursula Schulze-Gahmen, Ph.D.<br>Assistant Researcher<br>UC Berkeley, QB3<br>356 Stanley Hall #3220<br>Berkeley, CA 94720-3220<br><br>