[buster-discuss] DNA problem

Ed Pozharski epozh001 at umaryland.edu
Mon May 20 16:30:01 CEST 2013

I am trying to refine a model that contains DNA.  PDB file is, I
believe, in v3 nomenclature (DA/DT/DG/DC and O5' etc).  Refinement fails
early and I get the warning that the pdb file

"contains a majority of nucleic acids with ribose names O5' not O5*"

It suggests I run pdbvconv, which I do but that says

"v3 DNA names not detected"

and leaves the pdb file unchanged.  I didn't try renaming everything
back to v2 manually yet and did not really dig deep into the problem.
My hope is that I am missing something trivial that can be quickly

I am running v.2.1.0.



Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the great Tao is abandoned, Ideas of "humanitarianism" and         
                                               "righteousness" appear.
When intellectualism arises It is accompanied by great hypocrisy.
When there is strife within a family Ideas of "brotherly love" appear.
When nation is plunged into chaos Politicians become "patriotic".
------------------------------   / Lao Tse /

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