Hi Tim, just to spice your words up with some numbers....
You may also want to note that constrained hydrogen positions are a > crude approximation and only work with X-ray data where hydrogen atoms > have little impact on the data. This contribution can be as large as 1.5% difference in R-factor (with vs without H), as shown in Figure 2 (page 19; "On the contribution of hydrogen atoms to X-ray scattering"): http://phenix-online.org/newsletter/CCN_2012_01.pdf > Our comparison between hydrogen > restraints and constraints (http://dx.doi.org/10.1107/S1600576713027659) > report the greater quality of restraints vs. constraints when it comes > to neutron data, where hydrogen atoms do matter. I just re-refined (phenix.refine) all neutron structures available in PDB (for which I could extract diffraction data without manual labor; 55 in total) with two ways of handling H (D and H/D) atoms: a) refine H individually, and b) using riding model for H (rotatable H are adjusted to fit the map). In terms of Rfree and Rwork I don't see a huge difference. However, using riding model results in less overfitting: http://cci.lbl.gov/~afonine/tmp/r_stats.pdf This is not surprising given typical quality of neutron data: average (all neutron entries in PDB) completeness of neutron data sets is 76%, while average completeness of comparable X-ray data sets is 94% (page 21): http://phenix-online.org/presentations/latest/2012_afonine_ecm27-final.pdf All the best, Pavel
