[buster-discuss] buster and DNA?

Sabine Schneider sabine.schneider at cup.uni-muenchen.de
Fri Jun 11 17:16:49 CEST 2010


I am want to refine a protein-DNA complex in buster, but I am struggling 
with the nomenclature for DNA.
If I add DNA to the pdb file, buster fails with the following error 
message despite that there is a dictionary for the nucleotides:

WARNING : using geometric restraints for Gd from file
           this file was generated automatically using the
           CCP4/Refmac distributed dictionaries. Although we
           believe them to be of good quality, it was not
           checked manually. Therefore, it is supplied
           without any guarantee - if you prefer your own
           geometric restraints dictionary, please create it
           with one of the programs in the MakeTNT toolbox
           and supply it directly (see documentation).

I also tried changing it to GD, GUA, G as well as swapping the * for ', 
O1P to OP1 and so on....
In addition I generated a dictionary file using TNT which also failed.

Any help is much appreciated!


Dr. Sabine Schneider
Department of Chemistry
Butenandtstrasse 5-13, Building F
81377 Munich
Phone: +49 (0)89 2180 77752
Fax: +49 (0)89 2180 77756

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