Thanks to everyone for being such good sports!
It is good to know that there is still room for good-natured funny in
what can be stressful times.
Truth be told, I actually did do some experiments rounding off PDB
coordinates to the nearest A. You can try it with this one-line shell
command:
cat refined.pdb |\
awk '! /^ATOM|^HETAT/{print;next}\
{X=substr($0,31,8);Y=substr($0,39,8);Z=substr($0,47,8);\
pre=substr($0,1,30);post=substr($0,55)}\
{X=sprintf("%.0f",X);Y=sprintf("%.0f",Y);Z=sprintf("%.0f",Z)}\
{printf("%s%8.3f%8.3f%8.3f%s\n",pre,X,Y,Z,post)}' |\
cat > roundoff.pdb
These rounded-off structures look ... weird. And yes they really do
crash validation programs. Food for thought perhaps on what
"resolution", rmsd, and especially GDT_TS really mean?
-James Holton
MAD Scientist
On 4/1/2023 1:28 PM, Sweet, Robert wrote:
Knowing the author as I do, I checked the date and time, and wasn't fooled.
________________________________________
From: CCP4 bulletin board<CCP4BB@JISCMAIL.AC.UK> on behalf of Carter,
Charlie<car...@med.unc.edu>
Sent: Saturday, April 1, 2023 4:06 PM
To:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] new PDB file format
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<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
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