[phenixbb] Very low rmsd bond length

Luke Rice Luke.Rice at utsouthwestern.edu
Tue Jul 25 18:45:55 PDT 2017


I think a reasonable strategy is to acknowledge the concern, inform the reviewer about what changes if you do as asked, and use that as a data-driven way of justifying your decision.  I pasted below what worked for me when I had to address a similar issue in review.

> “the geometry is too tight”
> This is a frequently debated point among crystallographers, and there
> is no clear consensus. Given the challenges of our data (anisotropy,
> moderate completeness and resolution), we do not believe there is
> sufficient information content in the data to warrant significant
> deviations from ideal bond lengths and angles. Test refinements using
> different weights between the X-ray and stereochemical terms bear this
> out: allowing the geometry to relax by choosing a weight such that
> bond and angle deviations in the refined model are 0.01 Å and 1.3°
> results in Rfree decreasing by 0.3% while Rwork decreases 2.5%. Thus,
> we could have achieved a slightly lower Rfree at the expense of
> significantly greater decrease in Rwork. We prefer to maintain Rfree
> and (Rfree-Rwork) both as small as possible to minimize the
> possibility of overfitting.

Good luck,


> On Jul 25, 2017, at 5:52 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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