Jon, Riding hydrogens are *not* part of your model, they are part of the algorithm used to predict observations. Thus, the information is automatically included when you report the software used for refinement.
There are definitely some (many) parameters that are never included in the deposited pdb file. Some are built into software, some simply omitted. This may be wrong, but in my humble opinion riding hydrogens are easy to recalculate and thus their inclusion constitutes redundancy. BTW, I've seen some deposited pdb files which had water molecules given with hydrogens (e.g. 1aa7 - 2.1A resolution, and look - hydrogens have zero (!) B-factors). I think the best strategy is to give up hope that every structure in the PDB will conform to your set of ideals and realize that people are free to interpret their data the way they want (of course, assuming that nearly everyone else will disagree with at least some aspect of it). Ed. On Wed, 2008-12-17 at 15:53 -0800, Jonathan Winger wrote: > Hi all- > > Just wondering what the consensus is - should a structure refined with > riding hydrogens be deposited with the coordinates for the hydrogens > included? One could argue that, since they were used in the > refinement to obtain the model and statistics reported, they should be > included in the deposited pdb file. On the other hand, the presence > of hydrogens in the pdb file might lead some to think the hydrogens > were refined against density when they really weren't. Thoughts? > > Thanks, > Jon -- 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 /
