Hi Deng -
Can you tell why the reviewer was asking for the SA-omit map? Is there
some doubt about the conformation of your ssDNA, or even whether it is
present in the first place? Is there a question about the sequence, or
the sequence register (which nucleotides go in which positions)?
Even a poor-quality map should let you locate the phosphate backbone of
the DNA. This should convince most reviewers that the DNA is present
and in the general position you have modeled. You can't resolve
concerns about nucleotide base position or conformation without a better
quality map.
I imagine that you built the protein model first during your structure
determination, and only added the ssDNA later in the refinement. If
this is correct, you could present the maps from the last refinement
cycle before you added the DNA. This is even less model biased than
what the reviewer wants.
Hope that helps,
Matt
On 11/4/13 1:36 AM, dengzq1987 wrote:
Dear all,
Recently, I received the comments from referees, they asked for the
SA-omit map of the ssDNA of our protein-DNA complex. They said that
simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA
consists of seven thymidine nucleotide. Our data diffracted to
2.65A,but the data quality is not good and twin. We tried to produce
SA-omit map using phenix. The map is really bad. Does anyone have
suggestion to refine the map? Thank you!
Bests,
zq Deng
2013-11-04
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dengzq1987
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
