[phenixbb] Very low rmsd bond length

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jul 25 16:03:05 PDT 2017


Can you verify the RMSD range for bonds? Is it, "0.005-0.002" as stated or



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Jul 25, 2017 at 3:52 PM, Mark Saper <saper at umich.edu> wrote:

> Hi all,
> A reviewer points out that my refined structures (which have already been
> deposited in PDB) have very small RMSD values for bond lengths
> (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights
> should be decreased.  The weights were calculated with “Optimize XYZ
> Weight” option turned ON.  This seems to be the case with all of the
> structures that I have refined during the past 5 years.  My impression from
> previous discussions is that deriving explicit weights from these optimized
> ones is not straightforward and so I have never tried to relax the
> weights.  Moreover inspecting the optimization results in the log file,
> suggest that changing the weights to increase the RMSD would increase the
> Rfree. (I can post this if its helpful).
> How do I address the reviewer’s concerns?
> Thanks,
> Mark
> _______________________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, U-M Medical School
> Room 3220B, MSRB III   saper at umich.edu   +1 (734) 764-3353
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