And the good thing is we won’t be needed any more! - as alphafold structures will be just as good! ;)
Adrian Sent from my iPhone On 1 Apr 2023, at 18:06, Kolenko, Petr <00009d229ba2f5a3-dmarc-requ...@jiscmail.ac.uk> wrote: Dear James, what a great step forward! I see another point. In our programs, the coordinates will no longer need to be floats, doubles or whatever. They can easily be integers! I believe that this will dramatically speed up the process of refinement. 😉 Best regards, Petr ________________________________ Od: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> za uživatele James Holton <jmhol...@lbl.gov> Odesláno: sobota 1. dubna 2023 6:34 Komu: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Předmět: [ccp4bb] new PDB file format 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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/
