> - "bond length restraints" do not contribute to the scattering and > hence do not affect the R-factors, while H atoms do contribute to > scattering and therefore R-factors computed from the model with or > without hydrogens can be different (I spent a couple of months > implementing it in PHENIX and I can say for sure that the difference > is well noticeable).
Excellent point. But there are many things affecting R-factors not being reported. Do I have to deposit the bulk solvent mask? I think the fundamental question is why do you need to be able to reproduce the exact R-factors. Perhaps depositing FC and PHIC along with FP and SIGFP will solve your problem? > What about 50 years from now? Are you sure you will be able to dig out > that xxx.zzz.aaa version of that program, install it and run? I would > assume it will be much easier to take a complete model from data base. Another excellent point (assuming that 50 years from now I will care about similarly old structures :)). Don't get me wrong - I think it's important that deposited structures provide complete information about the model. But why are riding hydrogens so particularly important when reporting crystallization conditions is not mandatory? Or bulk solvent parameters? Or geometry restraints you used for the custom ligand (thus it's not in the standard libraries)? I did a quick (and dirty) survey of the PDB and found that less than 2% of structures report hydrogens. I didn't distinguish riding hydrogens and high-res structures, but even if they all are riding hydrogens they still almost always are not explicitly reported. What is interesting is the breakdown by the program used CNS/XPLOR 53% SHELX 29% (these might be mostly high-res) REFMAC 12% (some should be high-res, if not all) OTHER 7% (PHENIX, MAIN, MOLLY, PROFFT, PROLSQ) So it is safe to say that riding hydrogens are almost never intentionally included in the deposited model. Given that I found over 100 structures refined in X-PLOR with riding hydrogens reported, there must be some authors reading this list who may explain their reasoning. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
