[phenixbb] Building DNA

Paul Emsley 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.








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