Most non-structural users are familiar with the sequence of the proteins they are studying, and most software does at least display residue identity if you select an atom in a residue, so usually it is not necessary to do any cross checking besides selecting an atom in the residue and seeing what its residue name is. The chance of somebody misinterpreting a truncated Lys as Ala is, in my experience, much much lower than the chance they will trust the xyz coordinates of atoms with zero occupancy or high B factors.
What worries me the most is somebody designing a whole biological experiment around an over-interpretation of details that are implied by xyz coordinates of atoms, even if those atoms were not resolved in the maps. When this sort of error occurs it is a level of pain and wasted effort that makes the "pain" associated with having to build back in missing side chains look completely trivial. As long as the PDB file format is the way users get structural data, there is really no good way to communicate "atom exists with no reliable coordinates" to the user, given the diversity of software packages out there for reading PDB files and the historical lack of any standard way of dealing with this issue. Even if the file format is hacked there is no way to force all the existing software out there to understand the hack. A file format that isn't designed with this sort of feature from day one is not going to be fixable as a practical matter after so much legacy code has accumulated. -Eric On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote: > To the delete-the-atom-nik's: do you propose deleting the whole > residue or just the side chain? I can understand deleting the whole > residue, but deleting only the side chain seems to me to be placing a > stumbling block also, and even possibly confusing for an experienced > crystallographer: the .pdb says "lys" but it looks like an ala? Which > is it? I could imagine a lot of frustration-hours arising from this > practice, with people cross-checking sequences, looking in the methods > sections for mutations... > > JPK >
