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Yes, this can be done, but you need buccaneer 1.4, which I haven't released yet. We've seen significant benefits to preserving the heavy atoms through to the refinement, although the code has been written so that it can preserve DNA or any other know structure features as well. I'll try and put together a release next week so you can try it out. Kyle Dolan wrote: > Hello, > > I am trying to use Buccaneer to improve the model of a protein/DNA > complex which I solved recently. However, my initial attempt failed > because the program deleted the DNA chains and rebuilt protein chains in > their density. Is there a way to specify that the expected outcome > should contain a DNA ligand--either in the input model pdb or the input > sequence file--and to instruct the program to only work on the protein > during building? > > Thanks, > Kyle > > Kyle T. Dolan > Department of Biochemistry and Molecular Biology > The University of Chicago > [log in to unmask] <mailto:[log in to unmask]>