[phenixbb] Building DNA
paul.emsley at bioch.ox.ac.uk
Sat May 15 09:12:34 PDT 2010
Ralf W. Grosse-Kunstleve wrote:
> 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.
Coot understands these too (and converts the atom and residue names from
the model to match the dictionary) - except (I should add) the C7 of DT
which currently remains C5M.
>> 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.
Not PDB standard, no. Those name are what is in the refmac dictionary.
>> 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.
Paul Emsley knows that this is a failing - it is a matter of finding the
time to fix it. What is needed, I believe, is what Phenix does, and that
is an on-the-fly conversion of old PDB atom and residue dictionary names
to PDB version 3.0 names.
More information about the phenixbb