[phenixbb] Very low rmsd bond length

Mark Saper saper at umich.edu
Tue Jul 25 15:52:14 PDT 2017

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?  

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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