On Wednesday 17 December 2008 15:53:42 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?
It doesn't hurt to include them, bu I don't see much point in it. The riding-model parameters are sufficient to regenerate the hydrogen positions. Of the things one might worry about not including in a PDB file, I'm more concerned about the omission of scattering factors used for refinement and the continuing ambiguity of the precise meaning of the B factor reported in the ATOM record. And I am still scratching my head over the meaning of B factors attached to atoms with 0 occupancy. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
