Re: [ccp4bb] new PDB file format
Hi Robbie, Well, there is 1SRX (https://pdbe.org/1srx)) from 1976, CA-only, coordinate precision 0.05Å. The explanation is in the paper: "The maps were interpreted in terms of the known amino-acid sequence (2) and a skeletal model of one molecule was built with the Kendrew-type models using an optical comparator(13)." :-) (https://www.pnas.org/doi/epdf/10.1073/pnas.72.6.2305) --Gerard On Mon, 3 Apr 2023, Robbie Joosten wrote: WHAT_CHECK has a check for suspiciously rounded coordinates. I have never seen it triggered. Cheers, Robbie On 3 Apr 2023 10:11, James Holton wrote: 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 on behalf of Carter, Charlie 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 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 resol ution of the data. At long last, this age-old error is being corrected. From now on, coordinates will be listed to the nearest Angst rom 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 me thods 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 d oubt 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiN QyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTr UPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscm ail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are a vailable at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfravi FZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiN QyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTr UPapiNQyfrav
Re: [ccp4bb] new PDB file format
Thanks for reliably tickling our funny bones. BS From: James Holton Sent: Monday, April 3, 2023 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Cc: Sweet, Robert Subject: Re: [ccp4bb] new PDB file format 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 <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Carter, Charlie <mailto:car...@med.unc.edu> Sent: Saturday, April 1, 2023 4:06 PM To: CCP4BB@JISCMAIL.AC.UK<mailto: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 <mailto: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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available at http
Re: [ccp4bb] new PDB file format
WHAT_CHECK has a check for suspiciously rounded coordinates. I have never seen it triggered.Cheers,RobbieOn 3 Apr 2023 10:11, James Holton wrote: 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 on behalf of Carter, Charlie 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 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available at https://urldefense.com/v3/__
Re: [ccp4bb] new PDB file format
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 on behalf of Carter, Charlie 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 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members ofhttps://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted byhttps://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available athttps://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members ofhttps://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted byhttps://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available athttps://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message
Re: [ccp4bb] new PDB file format
Knowing the author as I do, I checked the date and time, and wasn't fooled. From: CCP4 bulletin board on behalf of Carter, Charlie 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 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ > > This message was issued to members of > https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ > , a mailing list hosted by > https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ > , terms & conditions are available at > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqN5MCD8m$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqMmvOHNo$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqCaWosgI$ , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!P4SdNyxKAPE!ECaCTTUpkh0GiKsgPTrUPapiNQyfraviFZihjo4vAPSbqkc4WhS0JVEl4ifyHotrj2BBLf-fqBmvnFst$ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
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 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=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=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/
Re: [ccp4bb] new PDB file format
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 <9d229ba2f5a3-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 za uživatele James Holton Odesláno: sobota 1. dubna 2023 6:34 Komu: 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=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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] new PDB file format
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 za uživatele James Holton Odesláno: sobota 1. dubna 2023 6:34 Komu: 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=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=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/
Re: [ccp4bb] new PDB file format
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 > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Ha ha! > >> On Sat, 1 Apr 2023 at 05:34, James Holton 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=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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] new PDB file format
Ha ha! On Sat, 1 Apr 2023 at 05:34, James Holton 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=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=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/
[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=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/