Well, what about getting the default settings on the major molecular
viewers to hide atoms with either occ=0 or b>cutoff ("novice mode?")?
While the b cutoff is still be tricky, I assume we could eventually
come to consensus on some reasonable cutoff (2 sigma from the mean?),
and then this approach would allow each free-spirited crystallographer
to keep his own preferred method of dealing with these troublesome
sidechains and nary a novice would be led astray....JPK On Sun, Apr 3, 2011 at 2:58 PM, Eric Bennett <er...@pobox.com> wrote: > 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 >> > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
