Ha ha! On Sat, 1 Apr 2023 at 05:34, James Holton <[email protected]> wrote:
> 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 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
