[buster-discuss] abasic refinement.

Francis Reyes Francis.Reyes at Colorado.EDU
Wed Jun 11 19:39:34 CEST 2014

Hi all,

I'm refining a protein:dna complex, and I'm yet uncertain to the sequence identity of the bases. Instead I'd like to to just simply place the phosphate backbone of the double stranded DNA and removed the bases (abasic DNA). 

I receive the following error: 

   >>> ab_pdb2tnt >>>
   >>> ab_pdb2tnt >>> Extracted from file 06/01-BUSTER/Rigid-1/ab_pdb2tnt.log : 
   >>> ab_pdb2tnt >>>
   >>> ab_pdb2tnt >>> WARNING : 10 atoms (out of 11) for residue "C" in PDB file
   >>> ab_pdb2tnt >>>           have names that are not present in the suggested
   >>> ab_pdb2tnt >>>           dictionary
   >>> ab_pdb2tnt >>>           /groups/gonen/home/reyesf/xtal/buster/tnt/data/nuclgeo.dat.
   >>> ab_pdb2tnt >>>           Therefore we will force the generation of a new
   >>> ab_pdb2tnt >>>           dictionary based on the current coordinates! For
   >>> ab_pdb2tnt >>>           details see below:

and then restraint generation by grade ends with error. 

Is it possible to refine abasic DNA? 



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