[phenixbb] occupancy refinement when alternate conformers clash

Jeff Headd jjheadd at lbl.gov
Wed Apr 13 10:10:54 PDT 2011

Hi Kendall,

I'm not entirely sure I understand the situation, but it sounds to me
like the you need to swap the A and B conformers on one side of the
base pair, which would allow the two A conformers to be paired and the
two B conformers to be paired. Is there a reason that you want the A
conformer from one base to be paired with the B conformer of the other
base? The A-A and B-B situation should work fine in refinement.


On Wed, Apr 13, 2011 at 9:58 AM, Kendall Nettles <knettles at scripps.edu> wrote:
> Hi,
> I am refining an RNA structure where on set of base pairs has alternate conformers, and the B alternates from the paired bases clash. That is, the structure should be viewed as A alternate in one base paired with B alternate in the other base. The refinement blew both B alts out of the density to prevent their clash.
> How can I fix this?
> Thanks for your help,
> Kendall Nettles
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