Re: [ccp4bb] "Atomic resolution"

[Robbie Joosten]

Hi Ivan,



I agree that the Hamilton test is quite useful in this context. We added it in 
PDB-REDO quite a while ago 
(http://www.cmbi.ru.nl/pdb_redo/reprints/CCP42011.pdf). Since that paper we 
have learned that at 18 reflections/atom is not enough to consistently pass the 
Hamilton test. We currently only accept anisotropic B-factors without testing 
at 30 reflections/atom.

I would argue that a 1% drop in R-free could still be the result of 
overfitting. After all, you are more than doubling your model parameters.



Cheers,

Robbie



Sent from my Windows 10 phone






From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Ivan Shabalin 
<iva...@iwonka.med.virginia.edu>
Sent: Friday, January 12, 2018 6:31:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] "Atomic resolution"

Perpetual topic!

The variety of opinions is amazing. Let me add my opinion here.

I like the definition set by Z. Dauter, G. Murshudov, and K. Wilson in
the International tables for Crystallography volume F (2001 edition),
section 18.4.1 "Definition of atomic resolution".

They define the atomic resolution as: when there are sufficient
accurately measured observables to justify the refinement of the ordered
part of the structure with full anisotropic ADPs.

Of course, it has a different meaning than the optical resolution, but
these tend to coincide.

There is no magic number that fits all structures. It depends on the
quality of data, completeness (especially in the highest shell), and
solvent content. 1.2 A is a rather conservative estimate.

To decide whether to use anisotropic ADPs or not, I like utilizing the
Hamilton R-value ratio test.  Basically, once you introduce extra
parameters, the drop of the R-free should be significant in relation to
the increase in the number of parameters.

The concept is very well explained in:

To B or not to B: a question of resolution?
https://www.ncbi.nlm.nih.gov/pubmed/22505267

The test is implemented in HKL3000, and probably, in other software.

If using the Hamilton test is not possible, i substitute the test with
two independent considerations (both are present in Hamilton test):

1) (Number of Unique reflections)/(Number of non-hydrogen atoms)> 18
should put me on rather safe side. This ratio stands for
"data-to-parameter ratio" = 2 or higher. One atom is defined by 9
parameters.

2) Drop of R-free has to be meaningful (significant). My rule of thumb
is that at least 0.5% percent is good. 1% is safer.

Ivan




With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908

On 01/11/2018 02:30 PM, Keller, Jacob wrote:
> Dear Crystallographers,
>
> Has there been a consensus as to what is meant by “atomic resolution?”
> Seems like the term is taken by various practitioners to mean different
> things.
>
> A related question: at what resolution are atoms “visible” using only
> the data? I have an empirical feeling that this would be around 1.5 Ang
> Bragg spacings, but on the other hand, one can contour up most maps and
> see individual atom peaks. I would be interested to hear a more rigorous
> way to think about this.
>
> All the best,
>
> Jacob Keller
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> (571)209-4000 x3159
>
> +
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the
> sender. If you received this message by mistake, please reply to this
> message and follow with its deletion, so that we can ensure such a
> mistake does not occur in the future.
>

Re: [ccp4bb] "Atomic resolution"

[Ivan Shabalin]

Perpetual topic!

The variety of opinions is amazing. Let me add my opinion here.

I like the definition set by Z. Dauter, G. Murshudov, and K. Wilson in 
the International tables for Crystallography volume F (2001 edition), 
section 18.4.1 "Definition of atomic resolution".


They define the atomic resolution as: when there are sufficient 
accurately measured observables to justify the refinement of the ordered 
part of the structure with full anisotropic ADPs.


Of course, it has a different meaning than the optical resolution, but 
these tend to coincide.


There is no magic number that fits all structures. It depends on the 
quality of data, completeness (especially in the highest shell), and 
solvent content. 1.2 A is a rather conservative estimate.


To decide whether to use anisotropic ADPs or not, I like utilizing the 
Hamilton R-value ratio test.  Basically, once you introduce extra 
parameters, the drop of the R-free should be significant in relation to 
the increase in the number of parameters.


The concept is very well explained in:

To B or not to B: a question of resolution?
https://www.ncbi.nlm.nih.gov/pubmed/22505267

The test is implemented in HKL3000, and probably, in other software.

If using the Hamilton test is not possible, i substitute the test with 
two independent considerations (both are present in Hamilton test):


1) (Number of Unique reflections)/(Number of non-hydrogen atoms)> 18 
should put me on rather safe side. This ratio stands for 
"data-to-parameter ratio" = 2 or higher. One atom is defined by 9 
parameters.


2) Drop of R-free has to be meaningful (significant). My rule of thumb 
is that at least 0.5% percent is good. 1% is safer.


Ivan




With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908

On 01/11/2018 02:30 PM, Keller, Jacob wrote:

Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic resolution?” 
Seems like the term is taken by various practitioners to mean different 
things.


A related question: at what resolution are atoms “visible” using only 
the data? I have an empirical feeling that this would be around 1.5 Ang 
Bragg spacings, but on the other hand, one can contour up most maps and 
see individual atom peaks. I would be interested to hear a more rigorous 
way to think about this.


All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of 
this message with any third party, without a written consent of the 
sender. If you received this message by mistake, please reply to this 
message and follow with its deletion, so that we can ensure such a 
mistake does not occur in the future.

Re: [ccp4bb] "Atomic resolution"

[mesters]

Atomic resolution or "the Sheldrick criterion" starts at 1.2 Å or 
better, 1.5 Å is too optimistic as the Bfactors are not zero as Vicotr 
pointed out, have a look at



 `Atomic resolution': a badly abused term in structural biology
 


and

Responses to/`Atomic resolution': a badly abused term in structural 
biology /






/
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It is invariably the case that high resolution X-ray structures show 
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coupling constants, 13C chemical shifts, and proton chemical shifts, 
than the corresponding NMR structures, including the very best ones. 
Hence, in most cases, a high-resolution crystal structure (< 2.0 Å)will 
provide a better description of the structure in solution than the 
corresponding NMR structure  (Kuszewski, Gronenborn & Clore, 1996, 
Protein Science 5:1067-80)

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Re: [ccp4bb] "Atomic resolution"

[Victor Lamzin]

Dear Jacob,

The resolution in reciprocal and real space was addressed by R. W. James 
in his paper 'False Detail in Three-Dimensional Fourier Representations 
of Crystal Structures' piblished in Acta Cryst. (1948). 1, 132-134. 
James showed that atomic density shape in the presence of series 
terminations is described by the Bessel function of zero order:


3*[sin(m) - m*cos(m)]/m^3
where m=2*Pi*r/dmin

This function is equal to 1 at the atomic centre (r=0) and decreases as 
r increases, then it oscillates. The function reduces to 0.5 for 
r/dmin=0.4. Therefore, the two equal atoms to be separated (in a sense 
of having a density in between lower than at their centres) the distance 
between them should be equal (or higher) than 2*dmin*0.4


Main chain C and O atoms separated by 1.23 A should be resolved if dmin 
is better than 1.55 A.


Two carbon sp3 atoms (distance 1.53 A) should be resolved if dmin is 
better than 1.9 A.


Indeed, as Thomas wrote, 1.5 A is about right.

The above is correct in the absence of atomic displacement parameters 
(Bfactor=0), for example for the normalised (sharpened) structure factor 
amplitudes. And, of course, for the complete and error-free diffraction 
data.


Victor



On 11/01/2018 21:07, Keller, Jacob wrote:


The reason behind this query is that I want to illustrate the power of 
prior knowledge in data analysis. I want to say something like “even 
though atoms cannot be directly observed at worse than X resolution, 
which represents Y% of the PDB, all of these data sets have been fit 
correctly with atomic models. This is due entirely to the power of the 
excellent priors which exist in crystallography.”


JPK

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the 
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*From:* Thomas Edwards [mailto:t.a.edwa...@leeds.ac.uk]
*Sent:* Thursday, January 11, 2018 2:59 PM
*To:* Keller, Jacob <kell...@janelia.hhmi.org>
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] "Atomic resolution"

Dear Jacob,

Ah... this old chestnut!

Current EM people say that they are at atomic resolution because they 
are building atomic models (naive??).


I have been criticised in the past for using the term with say 2.2A 
diffraction data. By co-authors and reviewers alike. When I was young 
and naive.


My (current) definition would be yours - visible with data.

I think 1.5A is about right for X-ray. Maybe higher res?

I’m sure there are lots of rigorous ways to think. I probably haven’t 
taken that route. However, I think it is a semantic problem that might 
benefit from some disambiguation rather than rigour.


It depends why you are asking the question...

Sorry..!

*/Ed is: Out and about.../*

*/Sent from iPhone6sPlus./*


On 11 Jan 2018, at 19:31, Keller, Jacob <kell...@janelia.hhmi.org 
<mailto:kell...@janelia.hhmi.org>> wrote:


Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic
resolution?” Seems like the term is taken by various practitioners
to mean different things.

A related question: at what resolution are atoms “visible” using
only the data? I have an empirical feeling that this would be
around 1.5 Ang Bragg spacings, but on the other hand, one can
contour up most maps and see individual atom peaks. I would be
interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the
recipient specified in message only. It is strictly forbidden to
share any part of this message with any third party, without a
written consent of the sender. If you received this message by
mistake, please reply to this message and follow with its
deletion, so that we can ensure such a mistake does not occur in
the future.

Re: [ccp4bb] "Atomic resolution"

[Bärbel Blaum]

Good topic, I just had a related thought: can I use the term in my NMR  
course to say it's the only spectroscopy that gives atomic resolution  
- meaning, here, that every NMR-active atom is distinguishable from  
its neighbours thanks to its unique chemical shift. At good enough  
resolution, i.e. field strength... Is it fair to use the term here or  
would you object since I am not talking about spacial resolution but  
something that could maybe be called 'chemical' resolution? But it is  
still 'atomic', isn't it?


Cheers, Bärbel

On 11 Jan 2018, at 19:31, Keller, Jacob  
> wrote:


Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic  
resolution?” Seems like the term is taken by various practitioners  
to mean different things.


A related question: at what resolution are atoms “visible” using  
only the data? I have an empirical feeling that this would be around  
1.5 Ang Bragg spacings, but on the other hand, one can contour up  
most maps and see individual atom peaks. I would be interested to  
hear a more rigorous way to think about this.


All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the  
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Re: [ccp4bb] "Atomic resolution"

[Graeme Winter]

Hi Jacob

If there’s fresh air between atoms in coot and you can assign the element by 
eye it’s atomic resolution to me

Probably corresponds to about 1.2A or thereabouts

I do however also respect the 0.8A limit used by our chemical crystallography 
colleagues

My two cents...

Best wishes Graeme

On 11 Jan 2018, at 19:31, Keller, Jacob 
> wrote:

Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic resolution?” Seems 
like the term is taken by various practitioners to mean different things.

A related question: at what resolution are atoms “visible” using only the data? 
I have an empirical feeling that this would be around 1.5 Ang Bragg spacings, 
but on the other hand, one can contour up most maps and see individual atom 
peaks. I would be interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.


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the message.
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Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] "Atomic resolution"

[Gloria Borgstahl]

My answer is not precise, I just try to give students something they
can remember, so they don't go and model water for example at an
inappropriate resolution.  Of course phasing matters as well.

On Thu, Jan 11, 2018 at 2:31 PM, Keller, Jacob  wrote:
>>I tell people it is when your resolution is less than the bond length that 
>>connects the two atoms.
>
> I thought this was sort of a pitfall, since the Bragg spacings don't 
> necessarily map on to conventional resolution. But it would fit the 1.5 Ang 
> estimate.
>
> Also, resolution would depend a lot on phase accuracy/precision, no?
>
> JPK
>
>
> On Thu, Jan 11, 2018 at 1:59 PM, Thomas Edwards  
> wrote:
>> Dear Jacob,
>>
>> Ah... this old chestnut!
>>
>> Current EM people say that they are at atomic resolution because they
>> are building atomic models (naive??).
>>
>> I have been criticised in the past for using the term with say 2.2A
>> diffraction data. By co-authors and reviewers alike. When I was young
>> and naive.
>>
>> My (current) definition would be yours - visible with data.
>> I think 1.5A is about right for X-ray. Maybe higher res?
>>
>> I’m sure there are lots of rigorous ways to think. I probably haven’t
>> taken that route. However, I think it is a semantic problem that might
>> benefit from some disambiguation rather than rigour.
>>
>> It depends why you are asking the question...
>>
>> Sorry..!
>>
>> Ed is: Out and about...
>> Sent from iPhone6sPlus.
>>
>> On 11 Jan 2018, at 19:31, Keller, Jacob  wrote:
>>
>> Dear Crystallographers,
>>
>>
>>
>> Has there been a consensus as to what is meant by “atomic resolution?”
>> Seems like the term is taken by various practitioners to mean different 
>> things.
>>
>>
>>
>> A related question: at what resolution are atoms “visible” using only
>> the data? I have an empirical feeling that this would be around 1.5
>> Ang Bragg spacings, but on the other hand, one can contour up most
>> maps and see individual atom peaks. I would be interested to hear a
>> more rigorous way to think about this.
>>
>>
>>
>> All the best,
>>
>>
>>
>> Jacob Keller
>>
>>
>>
>> +
>>
>> Jacob Pearson Keller
>>
>> Research Scientist / Looger Lab
>>
>> HHMI Janelia Research Campus
>>
>> 19700 Helix Dr, Ashburn, VA 20147
>>
>> (571)209-4000 x3159
>>
>> +
>>
>>
>>
>> The content of this email is confidential and intended for the
>> recipient specified in message only. It is strictly forbidden to share
>> any part of this message with any third party, without a written consent of 
>> the sender.
>> If you received this message by mistake, please reply to this message
>> and follow with its deletion, so that we can ensure such a mistake
>> does not occur in the future.
>>
>>

Re: [ccp4bb] "Atomic resolution"

[Keller, Jacob]

>I tell people it is when your resolution is less than the bond length that 
>connects the two atoms.

I thought this was sort of a pitfall, since the Bragg spacings don't 
necessarily map on to conventional resolution. But it would fit the 1.5 Ang 
estimate.

Also, resolution would depend a lot on phase accuracy/precision, no?

JPK


On Thu, Jan 11, 2018 at 1:59 PM, Thomas Edwards  wrote:
> Dear Jacob,
>
> Ah... this old chestnut!
>
> Current EM people say that they are at atomic resolution because they 
> are building atomic models (naive??).
>
> I have been criticised in the past for using the term with say 2.2A 
> diffraction data. By co-authors and reviewers alike. When I was young 
> and naive.
>
> My (current) definition would be yours - visible with data.
> I think 1.5A is about right for X-ray. Maybe higher res?
>
> I’m sure there are lots of rigorous ways to think. I probably haven’t 
> taken that route. However, I think it is a semantic problem that might 
> benefit from some disambiguation rather than rigour.
>
> It depends why you are asking the question...
>
> Sorry..!
>
> Ed is: Out and about...
> Sent from iPhone6sPlus.
>
> On 11 Jan 2018, at 19:31, Keller, Jacob  wrote:
>
> Dear Crystallographers,
>
>
>
> Has there been a consensus as to what is meant by “atomic resolution?” 
> Seems like the term is taken by various practitioners to mean different 
> things.
>
>
>
> A related question: at what resolution are atoms “visible” using only 
> the data? I have an empirical feeling that this would be around 1.5 
> Ang Bragg spacings, but on the other hand, one can contour up most 
> maps and see individual atom peaks. I would be interested to hear a 
> more rigorous way to think about this.
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> (571)209-4000 x3159
>
> +
>
>
>
> The content of this email is confidential and intended for the 
> recipient specified in message only. It is strictly forbidden to share 
> any part of this message with any third party, without a written consent of 
> the sender.
> If you received this message by mistake, please reply to this message 
> and follow with its deletion, so that we can ensure such a mistake 
> does not occur in the future.
>
>

Re: [ccp4bb] "Atomic resolution"

[Gloria Borgstahl]

I tell people it is when your resolution is less than the bond length
that connects the two atoms.

On Thu, Jan 11, 2018 at 1:59 PM, Thomas Edwards  wrote:
> Dear Jacob,
>
> Ah... this old chestnut!
>
> Current EM people say that they are at atomic resolution because they are
> building atomic models (naive??).
>
> I have been criticised in the past for using the term with say 2.2A
> diffraction data. By co-authors and reviewers alike. When I was young and
> naive.
>
> My (current) definition would be yours - visible with data.
> I think 1.5A is about right for X-ray. Maybe higher res?
>
> I’m sure there are lots of rigorous ways to think. I probably haven’t taken
> that route. However, I think it is a semantic problem that might benefit
> from some disambiguation rather than rigour.
>
> It depends why you are asking the question...
>
> Sorry..!
>
> Ed is: Out and about...
> Sent from iPhone6sPlus.
>
> On 11 Jan 2018, at 19:31, Keller, Jacob  wrote:
>
> Dear Crystallographers,
>
>
>
> Has there been a consensus as to what is meant by “atomic resolution?” Seems
> like the term is taken by various practitioners to mean different things.
>
>
>
> A related question: at what resolution are atoms “visible” using only the
> data? I have an empirical feeling that this would be around 1.5 Ang Bragg
> spacings, but on the other hand, one can contour up most maps and see
> individual atom peaks. I would be interested to hear a more rigorous way to
> think about this.
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> (571)209-4000 x3159
>
> +
>
>
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.
>
>

Re: [ccp4bb] "Atomic resolution"

[Diana Tomchick]

In the “good old days” we used to refer to “atomic resolution” as higher than 
1.0 Å (or more specifically, at least 0.8 Å resolution), e.g. the resolution 
obtained by most small molecule structures, where you get at least 10 times the 
number of observables per refined parameter, and thus could do full matrix 
least squares refinement of your model (including anisotropic thermal parameter 
refinement on all non-hydrogen atoms).

But then, I guess that just shows my age,

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
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On Jan 11, 2018, at 1:59 PM, Thomas Edwards 
> wrote:

Dear Jacob,

Ah... this old chestnut!

Current EM people say that they are at atomic resolution because they are 
building atomic models (naive??).

I have been criticised in the past for using the term with say 2.2A diffraction 
data. By co-authors and reviewers alike. When I was young and naive.

My (current) definition would be yours - visible with data.
I think 1.5A is about right for X-ray. Maybe higher res?

I’m sure there are lots of rigorous ways to think. I probably haven’t taken 
that route. However, I think it is a semantic problem that might benefit from 
some disambiguation rather than rigour.

It depends why you are asking the question...

Sorry..!

Ed is: Out and about...
Sent from iPhone6sPlus.

On 11 Jan 2018, at 19:31, Keller, Jacob 
> wrote:

Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic resolution?” Seems 
like the term is taken by various practitioners to mean different things.

A related question: at what resolution are atoms “visible” using only the data? 
I have an empirical feeling that this would be around 1.5 Ang Bragg spacings, 
but on the other hand, one can contour up most maps and see individual atom 
peaks. I would be interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

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Re: [ccp4bb] "Atomic resolution"

[Keller, Jacob]

The reason behind this query is that I want to illustrate the power of prior 
knowledge in data analysis. I want to say something like “even though atoms 
cannot be directly observed at worse than X resolution, which represents Y% of 
the PDB, all of these data sets have been fit correctly with atomic models. 
This is due entirely to the power of the excellent priors which exist in 
crystallography.”

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: Thomas Edwards [mailto:t.a.edwa...@leeds.ac.uk]
Sent: Thursday, January 11, 2018 2:59 PM
To: Keller, Jacob <kell...@janelia.hhmi.org>
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] "Atomic resolution"

Dear Jacob,

Ah... this old chestnut!

Current EM people say that they are at atomic resolution because they are 
building atomic models (naive??).

I have been criticised in the past for using the term with say 2.2A diffraction 
data. By co-authors and reviewers alike. When I was young and naive.

My (current) definition would be yours - visible with data.
I think 1.5A is about right for X-ray. Maybe higher res?

I’m sure there are lots of rigorous ways to think. I probably haven’t taken 
that route. However, I think it is a semantic problem that might benefit from 
some disambiguation rather than rigour.

It depends why you are asking the question...

Sorry..!
Ed is: Out and about...
Sent from iPhone6sPlus.

On 11 Jan 2018, at 19:31, Keller, Jacob 
<kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> wrote:
Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic resolution?” Seems 
like the term is taken by various practitioners to mean different things.

A related question: at what resolution are atoms “visible” using only the data? 
I have an empirical feeling that this would be around 1.5 Ang Bragg spacings, 
but on the other hand, one can contour up most maps and see individual atom 
peaks. I would be interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

Re: [ccp4bb] "Atomic resolution"

[Thomas Edwards]

Dear Jacob,

Ah... this old chestnut!

Current EM people say that they are at atomic resolution because they are 
building atomic models (naive??).

I have been criticised in the past for using the term with say 2.2A diffraction 
data. By co-authors and reviewers alike. When I was young and naive.

My (current) definition would be yours - visible with data.
I think 1.5A is about right for X-ray. Maybe higher res?

I’m sure there are lots of rigorous ways to think. I probably haven’t taken 
that route. However, I think it is a semantic problem that might benefit from 
some disambiguation rather than rigour.

It depends why you are asking the question...

Sorry..!

Ed is: Out and about...
Sent from iPhone6sPlus.

On 11 Jan 2018, at 19:31, Keller, Jacob 
> wrote:

Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic resolution?” Seems 
like the term is taken by various practitioners to mean different things.

A related question: at what resolution are atoms “visible” using only the data? 
I have an empirical feeling that this would be around 1.5 Ang Bragg spacings, 
but on the other hand, one can contour up most maps and see individual atom 
peaks. I would be interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

[ccp4bb] "Atomic resolution"

[Keller, Jacob]

Dear Crystallographers,

Has there been a consensus as to what is meant by "atomic resolution?" Seems 
like the term is taken by various practitioners to mean different things.

A related question: at what resolution are atoms "visible" using only the data? 
I have an empirical feeling that this would be around 1.5 Ang Bragg spacings, 
but on the other hand, one can contour up most maps and see individual atom 
peaks. I would be interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.