<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Pavel,<div><br></div><div>I haven't thought about it a lot, but here is my understanding of the effect. A symmetry axis (e.g., 2-fold) basically is the same as having 2 identical cells on top of each other, rotated 180 degrees. Imagine that cell 1 has random density. Then cell 2 has the same random density, rotated 180 degrees. Now add them together. At most points, the density from cell 1 and cell 2 are different, and the RMS of their sum is about sqrt(2) times the RMS of either one. On the other hand, at the symmetry axis, the density from cell 1 and cell 2 are identical, so that they always add constructively and the RMS is 2 times the RMS of either one. As you move away from the axis, the effect is smaller, and it decays away over the resolution of the map. Note that if you have a 3-fold, 4-fold or 6-fold, then the effect is even bigger.</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br><div><div>On Aug 10, 2010, at 9:07 AM, Pavel Afonine wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div> Hi Tom,<br><br>On 8/10/10 7:36 AM, Tom Terwilliger wrote:<br><blockquote type="cite">1. Yes, it is possible that the presence of a symmetry element very near the problematic area can make the density noisier. Normally this happens only right at the symmetry element however, not even a few A away.<br></blockquote><br>could you please explain why this happens?<br><br>Thanks!<br>Pavel.<br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div apple-content-edited="true"> <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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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:<a href="http://www.phenix-online.org">www.phenix-online.org</a><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></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>