[phenixbb] Building DNA

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Fri May 14 15:03:10 PDT 2010

Just a few quick comments for clarification:

> It seems like Autobuid uses the nomenclature DA, DC, DG
> and DT for the DNA bases while Phenix.Refine either doesn't like the
> nomenclature or the restraint files uses a different one. It still
> however lets me do the refinement...although I don't know if it just
> ignores the DNA part. Can someone enlighten me on this.

phenix.refine understands the whole variety RNA/DNA names.
The DA, DC, DG, DT names have been the standard PDB names as of summer 2007.

> Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA

These are older monomer library names; they've never been a standard.

> and doesn't like the above phenix style.

Paul Emsley knows best, but I believe current Coot versions understand
the 2007 standard PDB names, too.


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