<div dir="ltr">On Fri, Apr 18, 2014 at 6:53 AM, 李翔 <span dir="ltr"><<a href="mailto:lixiang1642@gmail.com" target="_blank">lixiang1642@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>I am working my low resolution data (6A) by MR and met a problem about DNA basepairing during refinement. I think so far everything looks OK except the bases flipped during the refinement. I added basepairing restraint for all bases, however, seems not help too much. Does anyone have experience on that?</div>
</div></blockquote><div><br></div><div>First of all, make sure you have real-space refinement turned off; this may be moving the DNA too aggressively. Second, it sounds like the base-pairing restraints may not be working correctly. If you send me the model (off-list!) I can take a look and see if there is a bug. The other option is to restrain the coordinates to the starting structure - I think the reference model restraints would be best but I'm not entirely sure if they work for DNA. (If not, you can use harmonic restraints, but these are less flexible.)</div>
<div><br></div><div>-Nat</div></div></div></div>