I fell for this momentarily, hence compliments to James. I was fooled by the absolutely sensible intro.
Charlie > On Apr 1, 2023, at 12:34 AM, 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/
