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It would be difficult because your protein probably affects the DNA conformation. Do you have some idea how your protein affects DNA conformation? But I think a brute force strategy trying every piece of DNA in the PDB as a template might work. Another approach would be to do MR using only segments of your DNA that might be straight B-DNA. ho --------------------------------------------------------------------- Date: Fri, 5 Dec 2008 16:32:14 -0600 From: UT MDACC <[log in to unmask]> Subject: MR with DNA Is there any existing example about anybody trying to do molecular replacement for a protein-DNA complex using any B-DNA from the pdb database. I am wondering 1) whether it is doable 2)if it is not doable, why not? Thanks in advance for the feedback