[phenixbb] DNA basepairing restraint refinement

Nathaniel Echols nechols at lbl.gov
Fri Apr 18 07:47:23 PDT 2014

On Fri, Apr 18, 2014 at 6:53 AM, 李翔 <lixiang1642 at gmail.com> wrote:

> 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?

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.)

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