<div>Hi Xun Lu,</div><div><br></div>Sounds like inverted oxygens on the phosphate backbone.<div>Go into Coot and find your DNA. Go 'Calculate' > 'Other Modelling Tools...' > 'Base Pair'. Now click one of your bases and go to the new base generated and compare the stereochemistry of OP1 and OP2 of your DNA and the one you've just made. I'll bet you anything that a few of them have been reversed and if you fix the naming you will get much better refinement.</div>
<div><br></div><div>Cheers,</div><div>Morten<br><br><div class="gmail_quote">On 31 January 2012 20:12, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On Tue, Jan 31, 2012 at 12:04 PM, Xun Lu <<a href="mailto:xluncsu@gmail.com">xluncsu@gmail.com</a>> wrote:<br>
> I am refining a protein-DNA complex structure at 2.9A resolution. The<br>
> R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA<br>
> is not well refined. Some sugar puckers are not right. The distances between<br>
> some base-paired bases are kind of short (~2.5A). I've tried including a<br>
> reference model for the DNA, or including a cif file, and I've also tried to<br>
> turn on the secondary_structure_restraints.... nothing worked. I must have<br>
> not done it in a correct way. But how to do it? And how to deal with sugar<br>
> puckers?<br>
<br>
</div>I don't know why the secondary structure restraints wouldn't work -<br>
could you please send me the PDB file off-list so I can see what's<br>
going wrong? �(No data necessary.)<br>
<br>
By the way, which version of Phenix are you using?<br>
<div class="im"><br>
> In refmac, I can set the distances between bases during the refinement, so<br>
> there must be a way to do it in phenix as well?<br>
<br>
</div>Yes, see here:<br>
<br>
<a href="https://www.phenix-online.org/version_docs/dev-973/refinement.htm#anch341" target="_blank">https://www.phenix-online.org/version_docs/dev-973/refinement.htm#anch341</a><br>
<br>
But hopefully the secondary structure restraints can be made to work.<br>
<br>
-Nat<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Morten K Gr�ftehauge, PhD�<div>Pohl Group</div><div>Durham University</div><br>
</div>