[ccp4bb] Position in CCP4 Core Group

[Eugene Krissinel - STFC UKRI]

Dear All,

A software engineer position is available in CCP4 Core group in Rutherford 
Appleton Laboratory, Oxfordshire, UK. Please see details here: 
https://careersportal.co.uk/UKRI-careers/jobs/software-engineer-computational-scientist-3024
 and let know anybody who may be interested.

Many thanks,

Eugene Krissinel.




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[ccp4bb] LN2 cryocooling system - manufacturers

[Kristof Van Hecke]

Dear all, 

By looking for manufacturers of LN2 cryocooling systems for in-house 
single-crystal X-ray diffractometers, I seems that Oxford Cryosystems is the 
only company nowadays providing such systems in Europe. In the past, we used to 
have such systems of Bruker and Oxford Instruments, but these all seem to be 
discontinued. 

Does anyone have an idea of other manufacturers of such dedicated systems 
similar to the Oxford cryostreams 700, 800, 1000, Cobra,.. etc. please? 
Any input would be highly appreciated. 

Thank you very much!

Regards

Kristof
  



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[ccp4bb] Structure prediction - waiting to happen

[Quyen Hoang]

Hi River,

What's in a name? That which we call a predicted structure
By any other name would still be uncertain until validated experimentally

Cheers,
Quyen

> On Apr 3, 2023, at 2:12 PM, Xiao, Chuan  wrote:
> 
> You raised a very good question: why we are asking this question now? Maybe 
> the answer is somewhere on the fact that Alphafold is a “revolution” in the 
> prediction field (borrow the term from resolution revolution in cryo-EM).
>  
> Anyway, when reading all these discussions, it made me think how I came to US 
> to learn how to solve a structure. My Master training is more like 
> bioinformatics. My second paper has a component of structural homology 
> modeling after sequencing some Rice genes. The paper was rejected by the 
> reviewers asking how I could proof my structural modeling (prediction) was 
> correct. At that time, I decided to learn how to solve the structure to proof 
> my prediction is correct. Now, it is interesting to see now the question is 
> on the other side. 
>  
> River  
>  
> From: CCP4 bulletin board  > On Behalf Of Quyen Hoang
> Sent: Sunday, April 2, 2023 10:20 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting 
> to happen
>  
> EXTERNAL EMAIL: This e-mail is from a sender outside of the UTEP system. Do 
> not click any links or open any attachments unless you trust the sender and 
> know the content is safe.
> Please forward suspicious emails to secur...@utep.edu 
>  or call 915.747.6324
> 
> Thank you for having this conversion.  
> I have heard this question more than once (why is experimental determination 
> needed when there is Alphafold) at grant study sections. Some came from 
> structural biologists, so hopefully, the discussion here would help them 
> also. 
> Computational modeling had existed for decades before Alphafold, and no one 
> ever questioned then, as far as I am aware, the need for experimental 
> determination of the modeled structures regardless of how accurate the 
> predicted models may have been (for example an MD state of a point mutation 
> using a high-resolution X-ray model as a starting model), so I am confused as 
> to why we are asking this question now. In my view, predicted model, as good 
> as it may be, is still a prediction. 
>  
> Cheers,
> Quyen
> 
> Quyen Hoang, PhD
> Associate Professor 
> Department of Biochemistry and Molecular Biology 
> Adjunct Associate Professor of Neurology
> Principal Investigator of the Stark Neurosciences Research Institute
> Indiana University School of Medicine
> 635 Barnhill Drive
> Medical Sciences Building, room MS0013C
> Indianapolis, IN 46202
> 317-274-4371 
>  
> 
> 
> On Apr 2, 2023, at 10:52 AM, Eugene Valkov  > wrote:
> 
>  
> It depends on the problem under investigation. For example, if you propose to 
> perform drug discovery with membrane proteins in a lipid/detergent 
> environment or study the structural organization of large ribonucleoprotein 
> assemblies, then AlphaFold will be of limited value and you should point this 
> out in the rebuttal.
>  
> If one of your aims is to study a protein, divide it into pieces, and solve 
> structures of domains, then this is justifiably questioned by reviewers in 
> light of the information provided by structure prediction. Perhaps in the 
> reviewer's opinion, there is no need to use substantial funds and time to 
> solve that structure. A more competitive proposal may then re-focus on 
> requesting resources for using the structural hypotheses to probe the 
> mechanism with more ambitious experimental structural aims or to take a 
> deeper dive into the function.
>  
> As Darwin said, it is not the strongest or the fastest (or even the most 
> intellectual!) that survives.
>  
> On Sun, 2 Apr 2023 at 11:28, Srivastava, Dhiraj  > wrote:
> That’s the point. All these predictions can not replace experiments and they 
> should be used only in the absence of experimental structures, that too with 
> caution. A biophysicist and structural biologist understand this but most of 
> the non-experts (including the reviewers of the grants from non-structural 
> biology study sections) don’t understand this and think that with alphafold, 
> there is no need for experimentally determined structures. That’s more 
> damaging than helpful. 
>  
>  
> From: CCP4 bulletin board  > on behalf of Eugene Valkov 
> mailto:eugene.val...@gmail.com>>
> Sent: Sunday, April 2, 2023 10:10 AM
> To: CCP4BB@JISCMAIL.AC.UK  
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting 
> to happen
>  
> Predicted structures lack the precision and accuracy of 
> experimentally-determined structures at high resolution with all the benefits 
> of 

Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to happen

[Xiao, Chuan]

You raised a very good question: why we are asking this question now? Maybe the 
answer is somewhere on the fact that Alphafold is a “revolution” in the 
prediction field (borrow the term from resolution revolution in cryo-EM).

Anyway, when reading all these discussions, it made me think how I came to US 
to learn how to solve a structure. My Master training is more like 
bioinformatics. My second paper has a component of structural homology modeling 
after sequencing some Rice genes. The paper was rejected by the reviewers 
asking how I could proof my structural modeling (prediction) was correct. At 
that time, I decided to learn how to solve the structure to proof my prediction 
is correct. Now, it is interesting to see now the question is on the other 
side. 

River

From: CCP4 bulletin board  On Behalf Of Quyen Hoang
Sent: Sunday, April 2, 2023 10:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to 
happen


EXTERNAL EMAIL: This e-mail is from a sender outside of the UTEP system. Do not 
click any links or open any attachments unless you trust the sender and know 
the content is safe.
Please forward suspicious emails to secur...@utep.edu 
or call 915.747.6324
Thank you for having this conversion.
I have heard this question more than once (why is experimental determination 
needed when there is Alphafold) at grant study sections. Some came from 
structural biologists, so hopefully, the discussion here would help them also.
Computational modeling had existed for decades before Alphafold, and no one 
ever questioned then, as far as I am aware, the need for experimental 
determination of the modeled structures regardless of how accurate the 
predicted models may have been (for example an MD state of a point mutation 
using a high-resolution X-ray model as a starting model), so I am confused as 
to why we are asking this question now. In my view, predicted model, as good as 
it may be, is still a prediction.

Cheers,
Quyen
Quyen Hoang, PhD
Associate Professor
Department of Biochemistry and Molecular Biology
Adjunct Associate Professor of Neurology
Principal Investigator of the Stark Neurosciences Research Institute
Indiana University School of Medicine
635 Barnhill Drive
Medical Sciences Building, room MS0013C
Indianapolis, IN 46202
317-274-4371



On Apr 2, 2023, at 10:52 AM, Eugene Valkov 
mailto:eugene.val...@gmail.com>> wrote:


It depends on the problem under investigation. For example, if you propose to 
perform drug discovery with membrane proteins in a lipid/detergent environment 
or study the structural organization of large ribonucleoprotein assemblies, 
then AlphaFold will be of limited value and you should point this out in the 
rebuttal.


If one of your aims is to study a protein, divide it into pieces, and solve 
structures of domains, then this is justifiably questioned by reviewers in 
light of the information provided by structure prediction. Perhaps in the 
reviewer's opinion, there is no need to use substantial funds and time to solve 
that structure. A more competitive proposal may then re-focus on requesting 
resources for using the structural hypotheses to probe the mechanism with more 
ambitious experimental structural aims or to take a deeper dive into the 
function.


As Darwin said, it is not the strongest or the fastest (or even the most 
intellectual!) that survives.

On Sun, 2 Apr 2023 at 11:28, Srivastava, Dhiraj 
mailto:dhiraj-srivast...@uiowa.edu>> wrote:
That’s the point. All these predictions can not replace experiments and they 
should be used only in the absence of experimental structures, that too with 
caution. A biophysicist and structural biologist understand this but most of 
the non-experts (including the reviewers of the grants from non-structural 
biology study sections) don’t understand this and think that with alphafold, 
there is no need for experimentally determined structures. That’s more damaging 
than helpful.



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Eugene Valkov 
mailto:eugene.val...@gmail.com>>
Sent: Sunday, April 2, 2023 10:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to 
happen


Predicted structures lack the precision and accuracy of 
experimentally-determined structures at high resolution with all the benefits 
of unbiased co-discovery of solvent molecules, ions, ligands, etc., bound to 
molecules of interest.


It is also true that AI-assisted structure prediction can be stunningly 
accurate to the level of correctly identifying interfacing residues between 
interacting proteins and accurately recapitulating the architectures of large, 
multi-domain complexes. AI-assisted structure prediction is immensely 
liberating in lowering the threshold to generate testable 

Re: [ccp4bb] new PDB file format

[Gerard Kleywegt]

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



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Re: [ccp4bb] new PDB file format

[Sweet, Robert]

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  
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] Issue about cif file of ligand

[Ning Li]

Wonderful! Grade solves my problem, thank you Pietro and Robbie!

Cheers

On Mon, Apr 3, 2023 at 12:38 PM Robbie Joosten 
wrote:

> Dear Ning,
>
> There is a separate bulletin board for anything Phenix. You can try the
> CCP4 program AceDRG to generate restraint from a SMILES string.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Ning Li
> > Sent: Monday, April 3, 2023 18:17
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] Issue about cif file of ligand
> >
> > Hi everyone,
> >
> > My crystal structure contains a ligand and I generated the cif file of
> the ligand
> > using phenix.elbow from the smiles file of the ligand. The ligand was
> drawn and
> > the smiles file was generated from
> > https://pubchem.ncbi.nlm.nih.gov//edit3/index.html. My problem is that
> the
> > double bond (shown in the picture) is longer than the single bond in the
> > generated elbow pdb file. Although the bond can be recognized correctly
> in the
> > Coot (display the correct double bond), the simulation software doesn't
> > recognize them correctly because of the bond length. In my theory, the
> double
> > bond of the ring should be shorter than the single bond, is there any
> reason
> > why phenix elbow generate this or any parameters I can set to overcome
> this?
> > Thank you for your suggestions.
> >
> > Ning
> >
> >
> >
> >
> > 
> >
> >
> > 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] Issue about cif file of ligand

[Robbie Joosten]

Dear Ning,

There is a separate bulletin board for anything Phenix. You can try the CCP4 
program AceDRG to generate restraint from a SMILES string. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ning Li
> Sent: Monday, April 3, 2023 18:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Issue about cif file of ligand
> 
> Hi everyone,
> 
> My crystal structure contains a ligand and I generated the cif file of the 
> ligand
> using phenix.elbow from the smiles file of the ligand. The ligand was drawn 
> and
> the smiles file was generated from
> https://pubchem.ncbi.nlm.nih.gov//edit3/index.html. My problem is that the
> double bond (shown in the picture) is longer than the single bond in the
> generated elbow pdb file. Although the bond can be recognized correctly in the
> Coot (display the correct double bond), the simulation software doesn't
> recognize them correctly because of the bond length. In my theory, the double
> bond of the ring should be shorter than the single bond, is there any reason
> why phenix elbow generate this or any parameters I can set to overcome this?
> Thank you for your suggestions.
> 
> Ning
> 
> 
> 
> 
> 
> 
> 
> 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] Issue about cif file of ligand

[Ning Li]

Hi everyone,

My crystal structure contains a ligand and I generated the cif file of the
ligand using phenix.elbow from the smiles file of the ligand. The ligand
was drawn and the smiles file was generated from
https://pubchem.ncbi.nlm.nih.gov//edit3/index.html. My problem is that the
double bond (shown in the picture) is longer than the single bond in the
generated elbow pdb file. Although the bond can be recognized correctly in
the Coot (display the correct double bond), the simulation software doesn't
recognize them correctly because of the bond length. In my theory, the
double bond of the ring should be shorter than the single bond, is there
any reason why phenix elbow generate this or any parameters I can set to
overcome this? Thank you for your suggestions.

Ning
[image: image.png]



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Re: [ccp4bb] new PDB file format

[Robbie Joosten]

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



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Re: [ccp4bb] new PDB file format

[James Holton]

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



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[ccp4bb] Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark.

[Bjørn Panyella Pedersen]

Dear colleagues,
Please pass this along anyone who might be interested. Thanks!
/Bjørn


Postdoctoral position in structure of sugar and phytohormone transporting 
membrane proteins at Aarhus University, Denmark.

online posting:
https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-sugar-and-phytohormone-transporting-membrane-proteins-at-aarhus-university-denmark

We are looking for a highly skilled and motivated postdoc with an interest in 
working on sugar and hormone transporting membrane transporters and preferably 
with a proven track record in the area of structural and/or functional analysis 
of membrane proteins.

The position will be open from summer 2023, but starting date is negotiable. 
Funding is available for at least 2 years of employment, with an extension 
possible for up to 4 years.

The position:
The position seeks to strengthen ongoing activities in the our group related to 
the function and mechanism of sugar-transporting and hormone-transporting 
membrane proteins in plants (pedersenlab.dk). Examples of our research can be 
found in:
Bavnhøj et al. “Molecular mechanism of sugar transport in plants unveiled by 
structures of glucose/H+ symporter STP10” Nature Plants 7 (2021)
Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” 
Nature 609 (2022).
The laboratory's interest is the interplay between structure and function of 
transmembrane transport processes with a focus on metabolite uptake systems and 
proton driven transport, and the methods uses are primarily structural biology 
(cryo-EM, crystallography) and biochemistry. The group is part of the Section 
of Structural Biology at Aarhus University.

The candidate:
A successful candidate has a relevant Ph.D. degree and a solid and documented 
background in structural biology, biochemistry and/or biophysics. Experience 
with membrane protein expression and purification is favored, and the candidate 
must demonstrate an ability and interest to work with membrane proteins with a 
structural aim. Applicants should be ambitious, show strong collaborative 
skills, and be able to take initiatives and responsibility within the work 
environment.

The successful candidate is offered:
- access to a well-developed research infrastructure.
- an exciting interdisciplinary environment with many national, international 
and industrial collaborators.
- a research climate inviting lively, open and critical discussion within and 
across different fields of research.
- a working environment with teamwork, close working relations, network 
activities among young scientists and social activities.
- a workplace characterized by professionalism, equality and a healthy 
work-life balance.

The city:
In Aarhus you have easy access to beautiful nature, an exciting culture and 
city life as well as a safe environment for children - a great place for the 
whole family. The city of Aarhus has everything you need: exciting national and 
international jobs, delightful residential areas, a rich cultural life, and 
beautiful surrounding landscape of woods and coastline that make Aarhus a 
wonderful place to live and work. See “life in Denmark” at Aarhus and 
surroundings for further details on the city and the university 
(https://international.au.dk/life/locations/aarhusandsurroundings).

Deadline:
All applications must be made online and received by 15. May. 2023.
See deails here:
https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-sugar-and-phytohormone-transporting-membrane-proteins-at-aarhus-university-denmark



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