Anyone who has ever had to lecture a student for writing their unit cell
lengths to dozens of decimal places is going to love the new PDB
format. It is more compact, more realistic, and less misleading to the
poor, downstream consumers of structural data.
Only a few structures in the PDB are better than 1.0 A, and none come
even close to 0.1 A. Nevertheless, the classic PDB file format always
listed atomic coordinates to three decimal places! That's implying a
precision of 0.001 A, which is not supported by the resolution of the
data. At long last, this age-old error is being corrected. From now
on, coordinates will be listed to the nearest Angstrom only.
An unexpected consequence of this is that R-free of a typical structure
is going to rise from the current ~20% to well into the 40%s. This is,
however, more consistent with high-impact structures published in
big-named journals using modern, better data collection methods like
XFELs and CryoEM, so we are going to call this an improvement. Besides,
R factors are just cosmetic anyway.
Updated molprobity scores are not yet available while the authors fix
bugs in their programs. Right now, they return errors with the new,
improved coordinates, such as:
line 272: 57012 Segmentation fault (core dumped)
So, just as we all must adapt to Python 3 this new standard I'm sure
will earn us all the thanks of future generations. They will no doubt be
very grateful that we took these pains to protect them from the dangers
of too many decimal places.
-James Holton
MAD Scientist
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