<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ursula,<div><br><div>It depends what the purpose of your averaging is...that routine is mainly designed to quickly show you what your averaged map would look like. If you are doing density modification then you can use</div><div><br></div><div> phenix.autobuild \</div><div> ncs_file=myncs.ncs_spec \</div><div> data=datafile.mtz \</div><div> input_map_file=working_map_coeffs.mtz \</div><div> seq_file = seq.dat \</div><div> maps_only=True</div><div><br></div><div>and that should run ncs averaging using both NCS groups. Let me know if that doesn't do what it is supposed to!</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br><div><div>On Dec 12, 2011, at 12:44 PM, Ursula Schulze-Gahmen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">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>
Fax: <a href="tel:505-665-3024" value="+15056653024" target="_blank">505-665-3024</a> SOLVE web site: <a href="http://solve.lanl.gov/" target="_blank">http://solve.lanl.gov</a><br>PHENIX web site: http:<a href="http://www.phenix-online.org/" target="_blank">www.phenix-online.org</a><br>
ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu/" target="_blank">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB" target="_blank">http://www.doe-mbi.ucla.edu/TB</a></div>
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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>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div><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: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:www.phenix-online.org<br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></span><br class="Apple-interchange-newline">
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