[buster-discuss] abasic refinement.

Ed Pozharski ccp4pozharski at gmail.com
Wed Jun 11 19:53:23 CEST 2014

You can make polyA and then delete "side chains" (in coot or with a grep one liner).  This way it will also be easier to build them back in (although you may need format conversion post-buster to get coot to work and I vaguely remember coot having some problems with truncation).

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<div>-------- Original message --------</div><div>From: Francis Reyes <Francis.Reyes at Colorado.EDU> </div><div>Date:06/11/2014  1:39 PM  (GMT-05:00) </div><div>To: buster-discuss at globalphasing.com </div><div>Subject: [buster-discuss] abasic refinement. </div><div>
</div>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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