Re: [ccp4bb] new PDB file format

[Sweet, Robert]

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
>
> 
>
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Re: [ccp4bb] new PDB file format

[Carter, Charlie]

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 
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Re: [ccp4bb] Structure prediction - waiting to happen

[Goldman, Adrian]

I think this is all true - and I’ve been putting things like this into my 
(failing) grants - but I get the dispiriting sense that the medics think (to 
borrow a line from hamlet) “the applicant doth protest too much methinks”. 

Well if as per James H today ;), we deposit coordinates to 1sf, alphafold will 
be just fine. 

Of course the coordinates won’t be of any use to anybody, but the pictures will 
be nice. 

Adrian 

Sent from my iPhone

> On 1 Apr 2023, at 21:39, Randy John Read  wrote:
> 
> There’s also this preprint with Tom Terwilliger as lead author: 
> https://www.biorxiv.org/content/10.1101/2022.11.21.517405v1. The title is 
> “AlphaFold predictions: great hypotheses but no match for experiment”.
> 
> Best wishes,
> 
> Randy
> 
>> On 1 Apr 2023, at 18:18, Savvas Savvides 
>> <9d24f7f13e09-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Dear Rams,
>> 
>> I salute you for sharing this.
>> 
>> Just a week ago, I also received a remark along these lines on a declined 
>> grant application. The remark was the only unfavourable point, which 
>> suggested that it must have weighed disproportionally towards the negative 
>> outcome. This was a two-stage evaluation process and the grant was cut in 
>> stage-1 where it was evaluated by a small group of evaluators, none of whom 
>> was a structural biologist/biochemist. Stage-2 would have involved peer 
>> review by international experts.
>> 
>> Despite my initial disbelief about what this remark might have caused and 
>> upon reflection, I realized that it might be time to become proactive in 
>> future applications in anticipation of the apparent growing trend towards 
>> such remarks and perceptions.
>> 
>> I think that a generalized form of preemptive text might not serve the 
>> purpose well, but perhaps well-articulated statements specific to the 
>> proposed biological problem at hand (perhaps aided by illustrations 
>> demonstrating the inability of structure prediction to address the problem 
>> at hand) might be the better way to go. Even though many of us who teach 
>> courses in experimental structural biology and structural bioinformatics at 
>> undergraduate and graduate levels are already actively addressing many of 
>> these issues, there is a much bigger and far more senior scientific 
>> population out there that makes important decisions on science 
>> policy/funding/infrastructures/evaluations/recruitment/etc that are not 
>> getting such educational exposure.
>> 
>> The following resources provide good material and starting points to reflect 
>> and elaborate upon.
>> 
>> The article by Perrakis and Sixma in EMBO Reports 
>> https://www.embopress.org/doi/full/10.15252/embr.202154046
>> 
>> The recent comment paper in Nature Methods by Thomas Jane
>> https://doi.org/10.1038/s41592-022-01760-4 
>> 
>> A correspondence in Science by Moore, Hendrickson, Henderson and Brunger
>> https://www.science.org/doi/10.1126/science.abn9422?url_ver=Z39.88-2003_id=ori:rid:crossref.org_dat=cr_pub%20%200pubmed
>> 
>> 
>> Best wishes
>> Savvas
>> 
>> 
>> 
>> Savvas Savvides
>> VIB Center for Inflammation Research
>> Ghent University, Dept. of Biochemistry & Microbiology
>> Technologiepark 71, 9052 Ghent, Belgium
>> 
>> Email: savvas.savvi...@ugent.be ; savvas.savvi...@irc.vib-ugent.be
>> Phone: +32 (0)472 928 519 (mobile) ; +32 (0)9 331 36 60 (office)
>> Web: https://savvideslab.sites.vib.be/en#/
>> 
 On 1 Apr 2023, at 16:57, Subramanian, Ramaswamy  
 wrote:
>>> 
>>> Ian,
>>> 
>>> Thank you.  This is not an April fools..  
>>> Rams
>>> subra...@purdue.edu
>>> 
>>> 
>>> 
 On Apr 1, 2023, at 10:46 AM, Ian Tickle  wrote:
 
  External Email: Use caution with attachments, links, or sharing data 
 
 
 
 Hi Ramaswamy
 
 I assume this is an April Fool's but it's still a serious question because 
 many reviewers who are not crystallographers or electron microscopists may 
 not fully appreciate the difference currently between the precision of 
 structures obtained by experimental and predictive methods, though the 
 latter are certainly catching up.  The answer of course lies in the mean 
 co-ordinate precision, related to the map resolution.
 
 Quoting https://people.cryst.bbk.ac.uk/~ubcg05m/precgrant.html :
 
 "The accuracy and precision required of an experimentally determined model 
 of a macromolecule depends on the biological questions being asked of the 
 structure.  Questions involving the overall fold of a protein, or its 
 topological similarity to other proteins, can be answered by structures of 
 fairly low precision such as those obtained from very low resolution X-ray 
 crystal diffraction data [or AlphaFold].  Questions involving reaction 
 mechanisms require much greater accuracy and precision as obtained from 
 well-refined, high-resolution X-ray structures, including proper 
 statistical analyses of the standard 

Re: [ccp4bb] Structure prediction - waiting to happen

[Randy John Read]

There’s also this preprint with Tom Terwilliger as lead author: 
https://www.biorxiv.org/content/10.1101/2022.11.21.517405v1. The title is 
“AlphaFold predictions: great hypotheses but no match for experiment”.

Best wishes,

Randy

> On 1 Apr 2023, at 18:18, Savvas Savvides 
> <9d24f7f13e09-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Dear Rams,
> 
> I salute you for sharing this.
> 
> Just a week ago, I also received a remark along these lines on a declined 
> grant application. The remark was the only unfavourable point, which 
> suggested that it must have weighed disproportionally towards the negative 
> outcome. This was a two-stage evaluation process and the grant was cut in 
> stage-1 where it was evaluated by a small group of evaluators, none of whom 
> was a structural biologist/biochemist. Stage-2 would have involved peer 
> review by international experts.
> 
> Despite my initial disbelief about what this remark might have caused and 
> upon reflection, I realized that it might be time to become proactive in 
> future applications in anticipation of the apparent growing trend towards 
> such remarks and perceptions.
> 
> I think that a generalized form of preemptive text might not serve the 
> purpose well, but perhaps well-articulated statements specific to the 
> proposed biological problem at hand (perhaps aided by illustrations 
> demonstrating the inability of structure prediction to address the problem at 
> hand) might be the better way to go. Even though many of us who teach courses 
> in experimental structural biology and structural bioinformatics at 
> undergraduate and graduate levels are already actively addressing many of 
> these issues, there is a much bigger and far more senior scientific 
> population out there that makes important decisions on science 
> policy/funding/infrastructures/evaluations/recruitment/etc that are not 
> getting such educational exposure.
> 
> The following resources provide good material and starting points to reflect 
> and elaborate upon.
> 
> The article by Perrakis and Sixma in EMBO Reports 
> https://www.embopress.org/doi/full/10.15252/embr.202154046
> 
> The recent comment paper in Nature Methods by Thomas Jane
> https://doi.org/10.1038/s41592-022-01760-4 
> 
> A correspondence in Science by Moore, Hendrickson, Henderson and Brunger
> https://www.science.org/doi/10.1126/science.abn9422?url_ver=Z39.88-2003_id=ori:rid:crossref.org_dat=cr_pub%20%200pubmed
> 
> 
> Best wishes
> Savvas
> 
> 
> 
> Savvas Savvides
> VIB Center for Inflammation Research
> Ghent University, Dept. of Biochemistry & Microbiology
> Technologiepark 71, 9052 Ghent, Belgium
> 
> Email: savvas.savvi...@ugent.be ; savvas.savvi...@irc.vib-ugent.be
> Phone: +32 (0)472 928 519 (mobile) ; +32 (0)9 331 36 60 (office)
> Web: https://savvideslab.sites.vib.be/en#/
> 
>> On 1 Apr 2023, at 16:57, Subramanian, Ramaswamy  wrote:
>> 
>> Ian,
>> 
>> Thank you.  This is not an April fools..  
>> Rams
>> subra...@purdue.edu
>> 
>> 
>> 
>>> On Apr 1, 2023, at 10:46 AM, Ian Tickle  wrote:
>>> 
>>>  External Email: Use caution with attachments, links, or sharing data 
>>> 
>>> 
>>> 
>>> Hi Ramaswamy
>>> 
>>> I assume this is an April Fool's but it's still a serious question because 
>>> many reviewers who are not crystallographers or electron microscopists may 
>>> not fully appreciate the difference currently between the precision of 
>>> structures obtained by experimental and predictive methods, though the 
>>> latter are certainly catching up.  The answer of course lies in the mean 
>>> co-ordinate precision, related to the map resolution.
>>> 
>>> Quoting https://people.cryst.bbk.ac.uk/~ubcg05m/precgrant.html :
>>> 
>>> "The accuracy and precision required of an experimentally determined model 
>>> of a macromolecule depends on the biological questions being asked of the 
>>> structure.  Questions involving the overall fold of a protein, or its 
>>> topological similarity to other proteins, can be answered by structures of 
>>> fairly low precision such as those obtained from very low resolution X-ray 
>>> crystal diffraction data [or AlphaFold].  Questions involving reaction 
>>> mechanisms require much greater accuracy and precision as obtained from 
>>> well-refined, high-resolution X-ray structures, including proper 
>>> statistical analyses of the standard uncertainties (s.u.'s) of atomic 
>>> positions and bond lengths.".
>>> 
>>> According to https://www.nature.com/articles/s41586-021-03819-2 :
>>> 
>>> The accuracy of AlphaFold structures at the time of writing (2021) was 
>>> around 1.0 Ang. RMSD for main-chain and 1.5 Ang. RMSD for side-chain atoms 
>>> and probably hasn't changed much since.  This is described as "highly 
>>> accurate"; however this only means that AlphaFold's accuracy is much higher 
>>> in comparison with other prediction methods, not in comparison with 
>>> experimental methods.  Also note that AlphaFold's accuracy is estimated by 
>>> comparison 

Re: [ccp4bb] Structure prediction - waiting to happen

[Savvas Savvides]

Dear Rams,

I salute you for sharing this.

Just a week ago, I also received a remark along these lines on a declined grant 
application. The remark was the only unfavourable point, which suggested that 
it must have weighed disproportionally towards the negative outcome. This was a 
two-stage evaluation process and the grant was cut in stage-1 where it was 
evaluated by a small group of evaluators, none of whom was a structural 
biologist/biochemist. Stage-2 would have involved peer review by international 
experts.

Despite my initial disbelief about what this remark might have caused and upon 
reflection, I realized that it might be time to become proactive in future 
applications in anticipation of the apparent growing trend towards such remarks 
and perceptions.

I think that a generalized form of preemptive text might not serve the purpose 
well, but perhaps well-articulated statements specific to the proposed 
biological problem at hand (perhaps aided by illustrations demonstrating the 
inability of structure prediction to address the problem at hand) might be the 
better way to go. Even though many of us who teach courses in experimental 
structural biology and structural bioinformatics at undergraduate and graduate 
levels are already actively addressing many of these issues, there is a much 
bigger and far more senior scientific population out there that makes important 
decisions on science policy/funding/infrastructures/evaluations/recruitment/etc 
that are not getting such educational exposure.

The following resources provide good material and starting points to reflect 
and elaborate upon.

The article by Perrakis and Sixma in EMBO Reports 
https://www.embopress.org/doi/full/10.15252/embr.202154046

The recent comment paper in Nature Methods by Thomas Jane
https://doi.org/10.1038/s41592-022-01760-4

A correspondence in Science by Moore, Hendrickson, Henderson and Brunger
https://www.science.org/doi/10.1126/science.abn9422?url_ver=Z39.88-2003_id=ori:rid:crossref.org_dat=cr_pub%20%200pubmed


Best wishes
Savvas



Savvas Savvides
VIB Center for Inflammation Research
Ghent University, Dept. of Biochemistry & Microbiology
Technologiepark 71, 9052 Ghent, Belgium

Email: savvas.savvi...@ugent.be ; 
savvas.savvi...@irc.vib-ugent.be
Phone: +32 (0)472 928 519 (mobile) ; +32 (0)9 331 36 60 (office)
Web: https://savvideslab.sites.vib.be/en#/

On 1 Apr 2023, at 16:57, Subramanian, Ramaswamy  wrote:

Ian,

Thank you.  This is not an April fools..
Rams
subra...@purdue.edu



On Apr 1, 2023, at 10:46 AM, Ian Tickle  wrote:

 External Email: Use caution with attachments, links, or sharing data 


Hi Ramaswamy

I assume this is an April Fool's but it's still a serious question because many 
reviewers who are not crystallographers or electron microscopists may not fully 
appreciate the difference currently between the precision of structures 
obtained by experimental and predictive methods, though the latter are 
certainly catching up.  The answer of course lies in the mean co-ordinate 
precision, related to the map resolution.

Quoting 
https://people.cryst.bbk.ac.uk/~ubcg05m/precgrant.html
 :

"The accuracy and precision required of an experimentally determined model of a 
macromolecule depends on the biological questions being asked of the structure. 
 Questions involving the overall fold of a protein, or its topological 
similarity to other proteins, can be answered by structures of fairly low 
precision such as those obtained from very low resolution X-ray crystal 
diffraction data [or AlphaFold].  Questions involving reaction mechanisms 
require much greater accuracy and precision as obtained from well-refined, 
high-resolution X-ray structures, including proper statistical analyses of the 
standard uncertainties (s.u.'s) of atomic positions and bond lengths.".

According to 
https://www.nature.com/articles/s41586-021-03819-2
 :

The accuracy of AlphaFold structures at the time of writing (2021) was around 
1.0 Ang. RMSD for main-chain and 1.5 Ang. RMSD for side-chain atoms and 
probably hasn't changed much since.  

Re: [ccp4bb] Structure prediction - waiting to happen

[Jurgen Bosch]

I was afraid of this happening at some point and decided to start a new career 
~ten years ago and use structures only as a tool and never put them into the 
centerpiece of a grant.

My fall back option is either a cocktail bar or starting a restaurant. The 
Triple M’s always work Mojito, Martini, Manhattan 

Jürgen 
> On Apr 1, 2023, at 11:29 AM, Dale Tronrud  wrote:
> 
> Hi,
> 
>   Just ask ChatGPT to write it for you!
> 
> Dale Tronrud
> 
> 
> 
> On 4/1/2023 5:06 AM, Subramanian, Ramaswamy wrote:
>> Dear All,
>> I am unsure if all other groups will get it - but I am sure this group will 
>> understand the frustration.
>> My NIH grant did not get funded.  A few genuine comments - they make 
>> excellent sense.  We will fix that.
>> One major comment is, “Structures can be predicted by alpfafold and other 
>> software accurately, so the effort put on the grant to get structures by 
>> X-ray crystallography/cryo-EM is not justified.”
>> The problem is when a company with billions of $$s develops a method and 
>> blasts it everywhere - the message is so pervasive…
>> *Question: I*s there a canned consensus paragraph that one can add with 
>> references to grants with structural biology (especially if the review group 
>> is not a structural biology group) to say why the most modern structure 
>> prediction programs are not a substitute for structural work?
>> Thanks.
>> Rams
>> subra...@purdue.edu
>> 
>> 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:
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> 
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Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to happen

[Srivastava, Dhiraj]

When I tested alpha fold on some of my proteins, it failed to predict the 
intramolecular interactions needed for their functions. Alphafold predicts the 
folds and overall structure of single domain and may be simple multi domain 
proteins but when conformational changes are needed for protein function, it 
fails to predict that. At-least it was the situation with some of my proteins. 
May be if somehow biochemical constraints are applied, it may predict the 
structure but you can not rely on alphafold to understand molecular mechanism 
of protein function. It’s too premature to think that alphafold can replace the 
need for experimental data.

Dhiraj



From: CCP4 bulletin board  on behalf of Ian Tickle 

Sent: Saturday, April 1, 2023 9:46 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] Re: [ccp4bb] Structure prediction - waiting to happen


Hi Ramaswamy

I assume this is an April Fool's but it's still a serious question because many 
reviewers who are not crystallographers or electron microscopists may not fully 
appreciate the difference currently between the precision of structures 
obtained by experimental and predictive methods, though the latter are 
certainly catching up.  The answer of course lies in the mean co-ordinate 
precision, related to the map resolution.

Quoting https://people.cryst.bbk.ac.uk/~ubcg05m/precgrant.html :

"The accuracy and precision required of an experimentally determined model of a 
macromolecule depends on the biological questions being asked of the structure. 
 Questions involving the overall fold of a protein, or its topological 
similarity to other proteins, can be answered by structures of fairly low 
precision such as those obtained from very low resolution X-ray crystal 
diffraction data [or AlphaFold].  Questions involving reaction mechanisms 
require much greater accuracy and precision as obtained from well-refined, 
high-resolution X-ray structures, including proper statistical analyses of the 
standard uncertainties (s.u.'s) of atomic positions and bond lengths.".

According to https://www.nature.com/articles/s41586-021-03819-2 :

The accuracy of AlphaFold structures at the time of writing (2021) was around 
1.0 Ang. RMSD for main-chain and 1.5 Ang. RMSD for side-chain atoms and 
probably hasn't changed much since.  This is described as "highly accurate"; 
however this only means that AlphaFold's accuracy is much higher in comparison 
with other prediction methods, not in comparison with experimental methods.  
Also note that AlphaFold's accuracy is estimated by comparison with the X-ray 
structure which remains the "gold standard"; there's no way (AFAIK) of 
independently assessing AlphaFold's accuracy or precision.

Quoting https://scripts.iucr.org/cgi-bin/paper?S0907444998012645 :

"Data of 0.94 A resolution for the 237-residue protein concanavalin A are used 
in unrestrained and restrained full-matrix inversions to provide standard 
uncertainties sigma(r) for positions and sigma(l) for bond lengths. sigma(r) is 
as small as 0.01 A for atoms with low Debye B values but increases strongly 
with B."

There's a yawning gap between 1.0 - 1.5 Ang. and 0.01 Ang.!  Perhaps AlphaFold 
structures should be deposited using James Holton's new PDB format (now that is 
an April Fool's !).

One final suggestion for a reference in your grant application: 
https://www.biorxiv.org/content/10.1101/2022.03.08.483439v2 .

Cheers

-- Ian


On Sat, 1 Apr 2023 at 13:06, Subramanian, Ramaswamy 
mailto:subra...@purdue.edu>> wrote:
Dear All,

I am unsure if all other groups will get it - but I am sure this group will 
understand the frustration.

My NIH grant did not get funded.  A few genuine comments - they make excellent 
sense.  We will fix that.

One major comment is, “Structures can be predicted by alpfafold and other 
software accurately, so the effort put on the grant to get structures by X-ray 
crystallography/cryo-EM is not justified.”

The problem is when a company with billions of $$s develops a method and blasts 
it everywhere - the message is so pervasive…

Question: Is there a canned consensus paragraph that one can add with 
references to grants with structural biology (especially if the review group is 
not a structural biology group) to say why the most modern structure prediction 
programs are not a substitute for structural work?

Thanks.


Rams
subra...@purdue.edu






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This message was 

Re: [ccp4bb] Structure prediction - waiting to happen

[Dale Tronrud]

Hi,

   Just ask ChatGPT to write it for you!

Dale Tronrud



On 4/1/2023 5:06 AM, Subramanian, Ramaswamy wrote:

Dear All,

I am unsure if all other groups will get it - but I am sure this group 
will understand the frustration.


My NIH grant did not get funded.  A few genuine comments - they make 
excellent sense.  We will fix that.


One major comment is, “Structures can be predicted by alpfafold and 
other software accurately, so the effort put on the grant to get 
structures by X-ray crystallography/cryo-EM is not justified.”


The problem is when a company with billions of $$s develops a method and 
blasts it everywhere - the message is so pervasive…


*Question: I*s there a canned consensus paragraph that one can add with 
references to grants with structural biology (especially if the review 
group is not a structural biology group) to say why the most modern 
structure prediction programs are not a substitute for structural work?


Thanks.


Rams
subra...@purdue.edu






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 







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Re: [ccp4bb] new PDB file format

[Goldman, Adrian]

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



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Re: [ccp4bb] new PDB file format

[Kolenko, Petr]

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



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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Re: [ccp4bb] Structure prediction - waiting to happen

[Subramanian, Ramaswamy]

Ian,

Thank you.  This is not an April fools..
Rams
subra...@purdue.edu



On Apr 1, 2023, at 10:46 AM, Ian Tickle  wrote:

 External Email: Use caution with attachments, links, or sharing data 


Hi Ramaswamy

I assume this is an April Fool's but it's still a serious question because many 
reviewers who are not crystallographers or electron microscopists may not fully 
appreciate the difference currently between the precision of structures 
obtained by experimental and predictive methods, though the latter are 
certainly catching up.  The answer of course lies in the mean co-ordinate 
precision, related to the map resolution.

Quoting https://people.cryst.bbk.ac.uk/~ubcg05m/precgrant.html :

"The accuracy and precision required of an experimentally determined model of a 
macromolecule depends on the biological questions being asked of the structure. 
 Questions involving the overall fold of a protein, or its topological 
similarity to other proteins, can be answered by structures of fairly low 
precision such as those obtained from very low resolution X-ray crystal 
diffraction data [or AlphaFold].  Questions involving reaction mechanisms 
require much greater accuracy and precision as obtained from well-refined, 
high-resolution X-ray structures, including proper statistical analyses of the 
standard uncertainties (s.u.'s) of atomic positions and bond lengths.".

According to https://www.nature.com/articles/s41586-021-03819-2 :

The accuracy of AlphaFold structures at the time of writing (2021) was around 
1.0 Ang. RMSD for main-chain and 1.5 Ang. RMSD for side-chain atoms and 
probably hasn't changed much since.  This is described as "highly accurate"; 
however this only means that AlphaFold's accuracy is much higher in comparison 
with other prediction methods, not in comparison with experimental methods.  
Also note that AlphaFold's accuracy is estimated by comparison with the X-ray 
structure which remains the "gold standard"; there's no way (AFAIK) of 
independently assessing AlphaFold's accuracy or precision.

Quoting https://scripts.iucr.org/cgi-bin/paper?S0907444998012645 :

"Data of 0.94 A resolution for the 237-residue protein concanavalin A are used 
in unrestrained and restrained full-matrix inversions to provide standard 
uncertainties sigma(r) for positions and sigma(l) for bond lengths. sigma(r) is 
as small as 0.01 A for atoms with low Debye B values but increases strongly 
with B."

There's a yawning gap between 1.0 - 1.5 Ang. and 0.01 Ang.!  Perhaps AlphaFold 
structures should be deposited using James Holton's new PDB format (now that is 
an April Fool's !).

One final suggestion for a reference in your grant application: 
https://www.biorxiv.org/content/10.1101/2022.03.08.483439v2 .

Cheers

-- Ian


On Sat, 1 Apr 2023 at 13:06, Subramanian, Ramaswamy 
mailto:subra...@purdue.edu>> wrote:
Dear All,

I am unsure if all other groups will get it - but I am sure this group will 
understand the frustration.

My NIH grant did not get funded.  A few genuine comments - they make excellent 
sense.  We will fix that.

One major comment is, “Structures can be predicted by alpfafold and other 
software accurately, so the effort put on the grant to get structures by X-ray 
crystallography/cryo-EM is not justified.”

The problem is when a company with billions of $$s develops a method and blasts 
it everywhere - the message is so pervasive…

Question: Is there a canned consensus paragraph that one can add with 
references to grants with structural biology (especially if the review group is 
not a structural biology group) to say why the most modern structure prediction 
programs are not a substitute for structural work?

Thanks.


Rams
subra...@purdue.edu






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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Re: [ccp4bb] Structure prediction - waiting to happen

[Ian Tickle]

Hi Ramaswamy

I assume this is an April Fool's but it's still a serious question because
many reviewers who are not crystallographers or electron microscopists may
not fully appreciate the difference currently between the precision of
structures obtained by experimental and predictive methods, though the
latter are certainly catching up.  The answer of course lies in the
mean co-ordinate precision, related to the map resolution.

Quoting https://people.cryst.bbk.ac.uk/~ubcg05m/precgrant.html :

"The accuracy and precision required of an experimentally determined model
of a macromolecule depends on the biological questions being asked of the
structure.  Questions involving the overall fold of a protein, or its
topological similarity to other proteins, can be answered by structures of
fairly low precision such as those obtained from very low resolution X-ray
crystal diffraction data [or AlphaFold].  Questions involving reaction
mechanisms require much greater accuracy and precision as obtained from
well-refined, high-resolution X-ray structures, including proper
statistical analyses of the standard uncertainties (*s.u.'s*) of atomic
positions and bond lengths.".

According to https://www.nature.com/articles/s41586-021-03819-2 :

The accuracy of AlphaFold structures at the time of writing (2021) was
around 1.0 Ang. RMSD for main-chain and 1.5 Ang. RMSD for side-chain atoms
and probably hasn't changed much since.  This is described as "highly
accurate"; however this only means that AlphaFold's accuracy is much higher
in comparison with other prediction methods, not in comparison with
experimental methods.  Also note that AlphaFold's accuracy is estimated by
comparison with the X-ray structure which remains the "gold standard";
there's no way (AFAIK) of independently assessing AlphaFold's accuracy or
precision.

Quoting https://scripts.iucr.org/cgi-bin/paper?S0907444998012645 :

"Data of 0.94 A resolution for the 237-residue protein concanavalin A are
used in unrestrained and restrained full-matrix inversions to provide
standard uncertainties sigma(r) for positions and sigma(l) for bond
lengths. sigma(r) is as small as 0.01 A for atoms with low Debye B values
but increases strongly with B."

There's a yawning gap between 1.0 - 1.5 Ang. and 0.01 Ang.!  Perhaps
AlphaFold structures should be deposited using James Holton's new PDB
format (now that is an April Fool's !).

One final suggestion for a reference in your grant application:
https://www.biorxiv.org/content/10.1101/2022.03.08.483439v2 .

Cheers

-- Ian


On Sat, 1 Apr 2023 at 13:06, Subramanian, Ramaswamy 
wrote:

> Dear All,
>
> I am unsure if all other groups will get it - but I am sure this group
> will understand the frustration.
>
> My NIH grant did not get funded.  A few genuine comments - they make
> excellent sense.  We will fix that.
>
> One major comment is, “Structures can be predicted by alpfafold and other
> software accurately, so the effort put on the grant to get structures by
> X-ray crystallography/cryo-EM is not justified.”
>
> The problem is when a company with billions of $$s develops a method and
> blasts it everywhere - the message is so pervasive…
>
> *Question: I*s there a canned consensus paragraph that one can add with
> references to grants with structural biology (especially if the review
> group is not a structural biology group) to say why the most modern
> structure prediction programs are not a substitute for structural work?
>
> Thanks.
>
>
> Rams
> subra...@purdue.edu
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Structure prediction - waiting to happen

[Bryan Lepore]

" Is there a canned consensus paragraph that one can add with references to 
grants "

How about:

“In general we look for a new law by the following process. First we guess it. 
Then we compute the consequences of the guess to see what would be implied if 
this law that we guessed is right. Then we compare the result of the 
computation to nature, with experiment or experience, compare it directly with 
observation, to see if it works. If it disagrees with experiment it is wrong. 
In that simple statement is the key to science. It does not make any difference 
how beautiful your guess is. It does not make any difference how smart you are, 
who made the guess, or what his name is – if it disagrees with experiment it is 
wrong. That is all there is to it.”

-Richard Feynman

The Character of Physical Law (1965)
Chapter 7, “Seeking New Laws”, p.150 (Modern Library edition, 1994)
ISBN 0-679-60127-9



> On Apr 1, 2023, at 08:06, Subramanian, Ramaswamy  wrote:
> 
> 
> Dear All,
> 
> I am unsure if all other groups will get it - but I am sure this group will 
> understand the frustration.
> 
> My NIH grant did not get funded.  A few genuine comments - they make 
> excellent sense.  We will fix that.
> 
> One major comment is, “Structures can be predicted by alpfafold and other 
> software accurately, so the effort put on the grant to get structures by 
> X-ray crystallography/cryo-EM is not justified.”
> 
> The problem is when a company with billions of $$s develops a method and 
> blasts it everywhere - the message is so pervasive…
> 
> Question: Is there a canned consensus paragraph that one can add with 
> references to grants with structural biology (especially if the review group 
> is not a structural biology group) to say why the most modern structure 
> prediction programs are not a substitute for structural work?
> 
> Thanks.
> 
> 
> Rams
> subra...@purdue.edu
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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[ccp4bb] Structure prediction - waiting to happen

[Subramanian, Ramaswamy]

Dear All,

I am unsure if all other groups will get it - but I am sure this group will 
understand the frustration.

My NIH grant did not get funded.  A few genuine comments - they make excellent 
sense.  We will fix that.

One major comment is, “Structures can be predicted by alpfafold and other 
software accurately, so the effort put on the grant to get structures by X-ray 
crystallography/cryo-EM is not justified.”

The problem is when a company with billions of $$s develops a method and blasts 
it everywhere - the message is so pervasive…

Question: Is there a canned consensus paragraph that one can add with 
references to grants with structural biology (especially if the review group is 
not a structural biology group) to say why the most modern structure prediction 
programs are not a substitute for structural work?

Thanks.


Rams
subra...@purdue.edu






To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] new PDB file format

[CCP4BB]

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/
> 
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Re: [ccp4bb] new PDB file format

[Eleanor Dodson]

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/
>



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