[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
resolved.

I am running v.2.1.0.

Cheers,

Ed.

-- 
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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