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On 12/16/10 06:47, Ian Tickle wrote: > > For the sake of argument let's say that 0.02 Ang is too big to be > rounding error. So if you see that big a shift then the intention of > the refinement program (or rather the programmer) which allowed such a > value to be appear in the output should be that it's real. If the > intention of the user was that the atom is actually on axis then the > program should not have allowed such a large shift, since it will be > interpreted as 'much bigger than rounding error' and therefore > 'significantly off-axis'. I would certainly hope that no one believes that the precision of the parameters in a PDB file are significant to the level of round-off error! It's bad enough that a small number of people take the three decimal points of precision in the PDB file seriously. When a person places an atom in a model they aren't stating a believe that that is the EXACT location of the atom, only that they believe the center of the locus of all equivalent atoms in the crystal falls near that spot. If it's 0.02 A from a special position (and the SU of the position is larger than that) then it might be on the special position and it might not. If I come across one of your models and you have an atom exactly on a special position (assuming you're able to do that with three decimal points in a PDB file) I'd still assume that you only intend that there is an atom in the vicinity of that point and it might be exactly on the axis but it might be a little off. All structural models are fuzzy. Dale Tronrud