My suspicions were raised when a post by James to this BB didn't run to several pages...
Harry -- Dr Harry Powell > On 1 Apr 2023, at 08:14, Eleanor Dodson > <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Ha ha! > >> On Sat, 1 Apr 2023 at 05:34, James Holton <jmhol...@lbl.gov> 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 ######################################################################## 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/
