Personally I think it is a _good_ thing that those missing atoms are a pain, because it helps ensure you are aware of the problem. As somebody who is in the business of supplying non-structural people with models, and seeing how those models are sometimes (mis)interpreted, I think it's better to inflict that pain than it is to present a model that non-structural people are likely to over-interpret.
The PDB provides various manipulated versions of crystal structures, such as biological assemblies. I don't think it would necessarily be a bad idea to build missing atoms back into those sorts of processed files but for the main deposited entry the best way to make sure the model is not abused is to leave out atoms that can't be modeled accurately. Just as an example since you mention surfaces, some of the people I work with calculate solvent accessible surface areas of individual residues for purposes such as engineering cysteines for chemical conjugation, and if residues are modeled into bogus positions just to say all the atoms are there, software that calculates per-residue SASA has to have a reliable way of knowing to ignore those atoms when calculating the area of neighboring residues. Ad hoc solutions like putting very large values in the B column are not clear cut for such a software program to interpret. Leaving the atom out completely is pretty unambiguous. -Eric On Mar 31, 2011, at 7:34 PM, Scott Pegan wrote: > I agree with Zbyszek with the modeling of side chains and stress the > following points: > > 1) It drives me nuts when I find that PDB is missing atoms from side chains. > This requires me to rebuild them to get any use out of the PDB such as > relevant surface renderings or electropotential plots. I am an experienced > structural biologist so that I can immediately identify that they have been > removed and can rebuild them. I feel sorry for my fellow scientists from > other biological fields that can't perform this task readability, thus > removing these atoms from a model limits their usefulness to a wider > scientific audience. > > 2) Not sure if any one has documented the percentage of actual side chains > missing from radiation damage versus heterogeneity in confirmation (i.e. > dissolved a crystal after collection and sent it to Mass Spec). Although > the former likely happens occasionally, my gut tells me that the latter is > significantly more predominant. As a result, absence of atoms from a side > chain in the PDB where the main chain is clearly visible in the electron > density might make for the best statistics for an experimental model, but > does not reflect a reality. > > Scott >
