[phenixbb] occupancy refinement when alternate conformers clash

Kendall Nettles knettles at scripps.edu
Wed Apr 13 09:58:42 PDT 2011

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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