Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Joel Sussman]

Following up what Kay Diederichs recently wrote, each page of Proteopedia that 
contains user added comments have a visible banner on the top,
e.g. see: https://proteopedia.org/w/2bs2
n.b. these user added comments are all signed, i.e. they are NOT anonymous, so 
it is a good location to consider user discussion on structural studies.

Joel


On 22Jul, 2019, at 14:16, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Proteopedia has this - see 
https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures

Kay

On Fri, 19 Jul 2019 17:42:33 +, Bonsor, Daniel 
mailto:dbon...@som.umaryland.edu>> wrote:

Would it be possible to add a public annotations section to the PDB, to allow 
us to potentially flag/warn whoever downloads that particular structure, there 
could be something wrong with it, such as wrong space group, no/poor density 
fitting for ligand. Something similar to PubPeer maybe?


Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Patrick Loll mailto:pjl...@gmail.com>>
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

The idea of contacting the editor (and/or author) is an excellent one, and 
indeed the correct thing to do scientifically. However, I�m disillusioned: I�ve 
been down this path before with a high-profile vanity journal, and while the 
editors paid lip service to the notion that the record should be corrected, in 
reality they led me on for the better part of a year, and got me to write up 
detailed analyses of why the ligand positioning was not justified, before 
eventually saying �no, we don�t see any need to publish a correction.� I 
speculate that the journal prefers not avoid corrections, for fear that too 
many corrections will make the journal a less desirable destination.

On 19 Jul 2019, at 11:23 AM, B�rbel Blaum 
mailto:baerbel.bl...@intherabio.com>> wrote:

Hi Rhys,
the reported B-factors for the �ligands� are all way below the reported 
B-factors for the protein chains, with the worst of the three complexes 
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight *one* 
striking feature of the data collection and refinement table. So even with the 
limited info normally available to reviewers this table should have raised a 
red flag. After the re-refinement suggested by others, i.e. your own proper 
assessment of the crystallographic data, if you do not find noteworthy density 
you may want to contact the article�s editor with your results. If you work in 
this field, i.e. really care about this paper scientifically and you are not 
afraid to confront the authors you could suggest writing a comment/direct 
response article but in my opinion that would only make sense if you can be 
sure beforehand that it will be linked visibly to the actual paper, else it 
will be a waste of time. And don�t forget that just because one or some of the 
authors did a bad job at the crystallographic end other findings of the paper 
might still be solid � in collaborations often one author is unable to 
critically evaluate another author�s contribution and this would not be the 
first case were good synthetic or biological work is presented along with a bad 
crystal structure.
By the way and a bit ironically this protein may have suffered bad 
crystallography/scientific practice before - I think it was one of the fake 
Krishna Murthy structures, right? The associated (now retracted) article I mean 
is here
https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub
[https://ars.els-cdn.com/content/image/S00222836.gif]
RETRACTED: Crystal structure of dengue virus NS3 protease in complex with a 
bowman-birk inhibitor: implications for flaviviral polyprotein processing and 
drug design - ScienceDirect - ScienceDirect.com | 
Science, health and medical journals, full text articles and 
books.
www.sciencedirect.com
COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center 
for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA 
2Department of Biochemistry and Molecular Biology, Kansas University Medical 
Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue viruses 
are members of the Flaviviridae and cause dengue fever Dengue fever and dengue 
hemorrhagic ...

Kind regards, B�rbel
---
B�rbel Blaum, PhD
Inthera Bioscience AG
Einsiedlerstrasse 34
CH-8820 Waedenswil
Switzerland
E-Mail: baerbel.bl...@intherabio.com
Phone: +41 43 477 94 

Re: [ccp4bb] Density questionable?

[Engi Hassaan]

We faced a similar situation recently where our molecular replacement
suggested 2 molecules in the asymmetric unit but the B factors of the
second chain were twice as large as the first protien chain. At a
resolution of 1.8 Å2 you could see the electron density for both chains. We
performed ARP/wARP and realized only part of this second chain is resolved
in our structure. It was model bias.

Best,
Engi


Engi Hassaan
PhD Student
Research Group of Prof. Dr. G. Klebe
Marburg, Germany


On Mon, Jul 22, 2019, 19:34 Bernhard Rupp  wrote:

> > Could there be two versions of each model: a "robustly-observed" and a
> "most-likely" version?
>
> We tried/suggested something in this spirit once. Not sure how it was
> received
> http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html
>
> Best, BR
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> Desk: (571)209-4000 x3159
> Cell: (301)592-7004
> +
>
> 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.
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Peer Mittl
> Sent: Monday, July 22, 2019 6:05 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Density questionable?
>
> Dear Colleagues,
>
> We are working on a structure where the density for a whole protein chain
> (>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3 Ang
> resolution). However, the initial difference density map and the feature
> enhanced map (normal 2fo-fc map to a minor extend) support the presence of
> this chain. Putting the chain seems equally wrong as not putting it.
> Putting
> it reduces Rfree by 0.3%. As a conservative researcher I feel tempted to
> deposit the structure without this highly mobile/weakly occupied chain, but
> other researchers may say "he has missed something". Handling this chain
> like a weakly occupied water is probably wrong, but what is the
> optimal/correct way? Is there a general opinion on how the escape this
> dilemma?
>
> All the best,
> Peer
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
>
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> 
>
> 
>
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To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] challenges in structural biology

[Nishant Varshney]

What about AI doing our job in the future?

https://www.nature.com/articles/d41586-019-01357-6?utm_source=Nature+Briefing_campaign=4c1d57fdf3-briefing-dy-20190722_medium=email_term=0_c9dfd39373-4c1d57fdf3-44201949

Best Regards
Nishant

On Mon, 22 Jul 2019 at 11:30 PM, Sarah Bowman 
wrote:

> I'd like to point out that the MAchine Recognition of Crystallization
> Outcomes (MARCO) makes a start to 'deep learning applied to crystallization
> outcomes', at least in terms of being able to classify drop images
> efficiently.
>
>
>
> There is obviously more work to be done to correlate these data with
> crystallization cocktail components (which Janet and Tom point out the
> difficulties with) and positive outcomes.  It seems the first step really
> needs to be consistent descriptions and vocabulary - I fully agree with
> Janet here!
>
>
>
> Reference on MARCO for those interested: Bruno AE, Charbonneau P, Newman
> J, Snell EH, So DR, Vanhoucke V, et al. (2018) Classification of
> crystallization outcomes using deep convolutional neural networks. PLoS ONE
> 13(6): e0198883. https://doi.org/10.1371/journal.pone.0198883
>
>
>
> Cheers,
>
> Sarah
>
>
>
> *Sarah EJ Bowman, PhD*
>
>
>
> Associate Research Scientist, Hauptman-Woodward Medical Research Institute
>
> Director, High-Throughput Crystallization Screening Center
>
> Research Associate Professor, Department of Biochemistry, University at
> Buffalo
>
>
>
> Research Webpage 
>
> www.getacrystal.org
>
>
>
> sbow...@hwi.buffalo.edu
> 716-898-8623
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Bernhard
> Rupp 
> *Organization: *k.k. Hofkristallamt
> *Reply-To: *"b...@hofkristallamt.org" 
> *Date: *Monday, July 22, 2019 at 1:42 PM
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: challenges in structural biology
>
>
>
> What about 'deep learning' applied to crystallization outcomes? Can it
> guide individual trials better than intuition? Can it find previously
> unknown promising combinations on a larger scale?
>
>
>
> I think several people were well aware of this need for some sort of sound
> machine learning already 15 years ago but we had no cloud based AI
>
> services thenmaybe it is time to pick this up - particularly if face
> recognition can classify the fine detail in faces maybe we finally could do
> this with drop images as well...
>
>
>
> A summary of the state of affairs then is here:
>
>
> http://www.ruppweb.org/cvs/br/rupp_2004_methods_predictive_models_crystallization.pdf
>
>
>
> LG BR
>
>
>
>
>
> Am 21.07.19 um 23:04 schrieb Artem Evdokimov:
>
> Dear Kay
>
>
>
> I disagree that 'magic bullet' is impossible. I think the definition is
> wrong here - magic bullet to me is a rational set of methods that (when
> executed with precision and care) enable crystallization to the maximum
> possible benefit. This includes everything - constructs, crystallization
> design, etc. Part of the magic bullet is also a precise knowledge when
> crystallization is unlikely (i.e. an actual proven predictor that
> consistently discriminates between "you're going to succeed if you work
> hard" and "it's doomed to fail, don't bother" scenarios in crystallization.
>
> The above is not sexy. It does not present itself as a lovely subject on
> which to have international cocktail parties with politicians delivering
> fancy speeches. But that is what is needed, and no one is funding that to
> the best of my knowledge.
>
> What needs to be done is a significant amount of testing, standardization,
> and methods development from the perspective of holistic outcome (i.e.
> crystals that work) - and none of the previously advertised 'magic bullets'
> work the way I just described.
>
> Having written this, I think you're right - this is a bit of a distraction
> from James' original point. However it's a valid opportunity for a lively
> discussion on its own :)
>
> Artem
>
> - Cosmic Cats approve of this message
>
> On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de 
> > wrote:
>
>  Dear Artem,
>
>  black or white is not my way of thinking, which is why I don't
> believe in Hannibal's approach when it comes to crystallization.
>
>  None of the magic bullets that were advertised over the past decades
> have proven generally applicable.  I believe more in incremental
> improvement which in this case includes a few biophysical characterization
> methods, possibly improved microfluidics or other apparatus, and expanded
> screens. And a lot of hard work, perseverance, intuition, frustration
>
>   tolerance. Nothing that really needs huge funding - of course it
> does need money, but just a  share of what is anyway needed for the usual
> lab work including expression, purification, functional characterization,
> binding studies and the like.
>
>  One area where a huge amount of money was burnt is crystallization in
> space, on board of 

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[John Berrisford]

Dear Harry

 

We will be shortly making it mandatory for depositors to provide a value for at 
least one of the merging statistics (Rmerge, Rpim, CC1/2 etc..). Most 
depositors do, but we want to ensure that all depositors do provide at least 
one value for a merging metric. 

 

We would welcome feedback if we should be stricter and require a (or more than 
one) specific metric (e.g. CC1/2) – please be aware that any required metric 
must be available from all merging/scaling software. 

 

Thanks

 

John

 

From: CCP4BB  
Sent: 22 July 2019 11:32
To: John Berrisford 
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Hi John

 

These are great, but the things that make me suspicious are the values of 
overall R(merge); these are tucked away in the full reports, rather than 
highlighted with all the other structural metrics in the validation sliders. It 
would be wonderful to be able to see at a glance where overall R(merge) values 
like these fit in with those of other deposited structures (even better if it 
could be drawn to the attention of authors before final deposition).

 

Kay and Gérard have already pointed out that the data processing here may have 
some issues.

 

Of course, those of us involved in teaching data processing have been 
emphasizing the importance of CC(1/2) rather than relying on R(merge) for 
yonks, but if CC(1/2) isn't given in the report it's all we have to go 

 

Harry

--

Dr Harry Powell


On 22 Jul 2019, at 10:05, John Berrisford mailto:j...@ebi.ac.uk> > wrote:

Dear Daniel

 

The issues you mentioned are highlighted in the wwPDB validation report

http://www.ebi.ac.uk/pdbe/entry-files/6mo0_full_validation.pdf

and global issues with the entry are highlighted in the validation sliders

http://www.ebi.ac.uk/pdbe/entry/pdb/6MO0

 

The validation sliders are shown on the entry pages at all wwPDB PDB sites 
(RCSB, PDBe and PDBj) and they all provide a link to download the wwPDB 
validation report directly from the entry page.

 

Regards

 

John

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Bonsor, Daniel
Sent: 19 July 2019 18:43
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Would it be possible to add a public annotations section to the PDB, to allow 
us to potentially flag/warn whoever downloads that particular structure, there 
could be something wrong with it, such as wrong space group, no/poor density 
fitting for ligand. Something similar to PubPeer maybe? 

 

Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201

 


  _  


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Patrick Loll mailto:pjl...@gmail.com> >
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK   
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 

 

The idea of contacting the editor (and/or author) is an excellent one, and 
indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve 
been down this path before with a high-profile vanity journal, and while the 
editors paid lip service to the notion that the record should be corrected, in 
reality they led me on for the better part of a year, and got me to write up 
detailed analyses of why the ligand positioning was not justified, before 
eventually saying “no, we don’t see any need to publish a correction.” I 
speculate that the journal prefers not avoid corrections, for fear that too 
many corrections will make the journal a less desirable destination.

> On 19 Jul 2019, at 11:23 AM, Bärbel Blaum   > wrote:
> 
> Hi Rhys,
> the reported B-factors for the “ligands” are all way below the reported 
> B-factors for the protein chains, with the worst of the three complexes 
> reporting unitless numbers 23.2 and 64.8, respectively, just to highlight 
> *one* striking feature of the data collection and refinement table. So even 
> with the limited info normally available to reviewers this table should have 
> raised a red flag. After the re-refinement suggested by others, i.e. your own 
> proper assessment of the crystallographic data, if you do not find noteworthy 
> density you may want to contact the article’s editor with your results. If 
> you work in this field, i.e. really care about this paper scientifically and 
> you are not afraid to confront the authors you could suggest writing a 
> comment/direct response article but in my opinion that would only make sense 
> if you can be sure beforehand that it will be linked visibly to the actual 
> paper, else it will be a waste of time. And don’t forget that just because 
> one or some of the authors did a bad job at the crystallographic end other 
> findings of the paper might still be 

Re: [ccp4bb] challenges in structural biology

[Sarah Bowman]

I'd like to point out that the MAchine Recognition of Crystallization Outcomes 
(MARCO) makes a start to 'deep learning applied to crystallization outcomes', 
at least in terms of being able to classify drop images efficiently.

There is obviously more work to be done to correlate these data with 
crystallization cocktail components (which Janet and Tom point out the 
difficulties with) and positive outcomes.  It seems the first step really needs 
to be consistent descriptions and vocabulary - I fully agree with Janet here!

Reference on MARCO for those interested: Bruno AE, Charbonneau P, Newman J, 
Snell EH, So DR, Vanhoucke V, et al. (2018) Classification of crystallization 
outcomes using deep convolutional neural networks. PLoS ONE 13(6): e0198883. 
https://doi.org/10.1371/journal.pone.0198883

Cheers,
Sarah

Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center
Research Associate Professor, Department of Biochemistry, University at Buffalo

Research Webpage
www.getacrystal.org

sbow...@hwi.buffalo.edu
716-898-8623


From: CCP4 bulletin board  on behalf of Bernhard Rupp 

Organization: k.k. Hofkristallamt
Reply-To: "b...@hofkristallamt.org" 
Date: Monday, July 22, 2019 at 1:42 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: challenges in structural biology

What about 'deep learning' applied to crystallization outcomes? Can it guide 
individual trials better than intuition? Can it find previously unknown 
promising combinations on a larger scale?

I think several people were well aware of this need for some sort of sound 
machine learning already 15 years ago but we had no cloud based AI
services thenmaybe it is time to pick this up - particularly if face 
recognition can classify the fine detail in faces maybe we finally could do 
this with drop images as well...

A summary of the state of affairs then is here:
http://www.ruppweb.org/cvs/br/rupp_2004_methods_predictive_models_crystallization.pdf

LG BR


Am 21.07.19 um 23:04 schrieb Artem Evdokimov:
Dear Kay

I disagree that 'magic bullet' is impossible. I think the definition is wrong 
here - magic bullet to me is a rational set of methods that (when executed with 
precision and care) enable crystallization to the maximum possible benefit. 
This includes everything - constructs, crystallization design, etc. Part of the 
magic bullet is also a precise knowledge when crystallization is unlikely (i.e. 
an actual proven predictor that consistently discriminates between "you're 
going to succeed if you work hard" and "it's doomed to fail, don't bother" 
scenarios in crystallization.
The above is not sexy. It does not present itself as a lovely subject on which 
to have international cocktail parties with politicians delivering fancy 
speeches. But that is what is needed, and no one is funding that to the best of 
my knowledge.
What needs to be done is a significant amount of testing, standardization, and 
methods development from the perspective of holistic outcome (i.e. crystals 
that work) - and none of the previously advertised 'magic bullets' work the way 
I just described.
Having written this, I think you're right - this is a bit of a distraction from 
James' original point. However it's a valid opportunity for a lively discussion 
on its own :)
Artem
- Cosmic Cats approve of this message
On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de> 
>
 wrote:
 Dear Artem,
 black or white is not my way of thinking, which is why I don't believe in 
Hannibal's approach when it comes to crystallization.
 None of the magic bullets that were advertised over the past decades have 
proven generally applicable.  I believe more in incremental improvement which 
in this case includes a few biophysical characterization methods, possibly 
improved microfluidics or other apparatus, and expanded screens. And a lot of 
hard work, perseverance, intuition, frustration
  tolerance. Nothing that really needs huge funding - of course it does 
need money, but just a  share of what is anyway needed for the usual lab work 
including expression, purification, functional characterization, binding 
studies and the like.
 One area where a huge amount of money was burnt is crystallization in 
space, on board of e.g. the spacelab and ISS. This is for me an example of a 
mis-led approach to throw money at a difficult problem, with the expectation of 
a solution. Science does not work like that, and money in this case seems more 
to be the problem than the solution.
 This example may illustrate a certain failure of us scientists to resist 
the temptation to promise unrealistic outcomes when confronted with money 
provided for political 

Re: [ccp4bb] challenges in structural biology

[Bernhard Rupp]

> What about 'deep learning' applied to crystallization outcomes? Can it guide 
> individual trials better than intuition? Can it find previously unknown 
> promising combinations on a larger scale?

I think several people were well aware of this need for some sort of sound 
machine learning already 15 years ago but we had no cloud based AI
services thenmaybe it is time to pick this up - particularly if face 
recognition can classify the fine detail in faces maybe we finally could do 
this with drop images as well...

A summary of the state of affairs then is here:
http://www.ruppweb.org/cvs/br/rupp_2004_methods_predictive_models_crystallization.pdf

LG BR


Am 21.07.19 um 23:04 schrieb Artem Evdokimov:
> Dear Kay
>  
> 
> I disagree that 'magic bullet' is impossible. I think the definition is wrong 
> here - magic bullet to me is a rational set of methods that (when executed 
> with precision and care) enable crystallization to the maximum possible 
> benefit. This includes everything - constructs, crystallization design, etc. 
> Part of the magic bullet is also a precise knowledge when crystallization is 
> unlikely (i.e. an actual proven predictor that consistently discriminates 
> between "you're going to succeed if you work hard" and "it's doomed to fail, 
> don't bother" scenarios in crystallization.
> 
> The above is not sexy. It does not present itself as a lovely subject on 
> which to have international cocktail parties with politicians delivering 
> fancy speeches. But that is what is needed, and no one is funding that to the 
> best of my knowledge.
> 
> What needs to be done is a significant amount of testing, standardization, 
> and methods development from the perspective of holistic outcome (i.e. 
> crystals that work) - and none of the previously advertised 'magic bullets' 
> work the way I just described.
> 
> Having written this, I think you're right - this is a bit of a distraction 
> from James' original point. However it's a valid opportunity for a lively 
> discussion on its own :)
> 
> Artem
> 
> - Cosmic Cats approve of this message
> 
> 
> On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> 
> wrote:
> 
> Dear Artem,
> 
> black or white is not my way of thinking, which is why I don't believe in 
> Hannibal's approach when it comes to crystallization.
> 
> None of the magic bullets that were advertised over the past decades have 
> proven generally applicable.  I believe more in incremental improvement which 
> in this case includes a few biophysical characterization methods, possibly 
> improved microfluidics or other apparatus, and expanded screens. And a lot of 
> hard work, perseverance, intuition, frustration
>  tolerance. Nothing that really needs huge funding - of course it does 
> need money, but just a  share of what is anyway needed for the usual lab work 
> including expression, purification, functional characterization, binding 
> studies and the like.
> 
> One area where a huge amount of money was burnt is crystallization in 
> space, on board of e.g. the spacelab and ISS. This is for me an example of a 
> mis-led approach to throw money at a difficult problem, with the expectation 
> of a solution. Science does not work like that, and money in this case seems 
> more to be the problem than the solution.
> 
> This example may illustrate a certain failure of us scientists to resist 
> the temptation to promise unrealistic outcomes when confronted with money 
> provided for political reasons, which ultimately undermines our credibility. 
> But this takes us away from James' points.
> 
> best,
> 
> Kay
> 
> On Sun, 21 Jul 2019 16:06:48 -0400, Artem Evdokimov 
> mailto:artem.evdoki...@gmail.com>> wrote:
> 
> >Dear Kay,
> >
> >Even the small, badly diffracting and 'messed up' crystals are still
> >crystals. There is literally a phase transition (pun very much intended)
> >between growing *usable crystals* versus *having no crystals* (or having
> >crystals that do not qualify as 'diffraction quality' even under the most
> >favorable light). Points 2-9 fall into the 'I have crystals' bucket and
> >everything else is in the 'I have no crystals' bucket.
> >
> >I am being deliberately black and white of course.
> >
> >As to whether huge funding would help to bridge the 'phase gap' - to me
> >this is a purely theoretical question since to the best of my knowledge
> >there never was a 'huge funding' for this particular problem :) And if it
> >is true that the general belief in the art is that crystallization is not
> >worth investing into because there's no hope in it then of course it is a
> >self-fulfilling prophesy.
> >
> >There is an unresolved dichotomy buried in the sentiment above: it seems
> >that we (the community of structural biologists) more or less believe 
> that
> >crystallization research is not 

Re: [ccp4bb] Density questionable?

[Bernhard Rupp]

> Could there be two versions of each model: a "robustly-observed" and a
"most-likely" version?

We tried/suggested something in this spirit once. Not sure how it was
received
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html

Best, BR
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

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-Original Message-
From: CCP4 bulletin board  On Behalf Of Peer Mittl
Sent: Monday, July 22, 2019 6:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Density questionable?

Dear Colleagues,

We are working on a structure where the density for a whole protein chain
(>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3 Ang
resolution). However, the initial difference density map and the feature
enhanced map (normal 2fo-fc map to a minor extend) support the presence of
this chain. Putting the chain seems equally wrong as not putting it. Putting
it reduces Rfree by 0.3%. As a conservative researcher I feel tempted to
deposit the structure without this highly mobile/weakly occupied chain, but
other researchers may say "he has missed something". Handling this chain
like a weakly occupied water is probably wrong, but what is the
optimal/correct way? Is there a general opinion on how the escape this
dilemma?

All the best,
Peer



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Re: [ccp4bb] Density questionable?

[Keller, Jacob]

This is the old question of what a structural model represents. One perspective 
is that it represents the things one is certain about above some threshold, 
from the crystallographic data and maps alone. The other perspective is that it 
represents the most likely guess of what is actually there. I prefer the second 
"most likely" approach since it incorporates more information, namely the 
knowledge of what's in the solutions, the way proteins pack, the protein's 
sequence, etc. And everyone agrees to the use of such priors when it comes to 
bond lengths and similar. I guess it boils down to the weighting of prior 
information.

A problem arises, however, when users from one camp look at models from the 
other camp, and I do not really have a solution to this, especially as the two 
camps don't tend to see both sides of the question. Could there be two versions 
of each model: a "robustly-observed" and a "most-likely" version?

Maybe this debate could also be raised at the Holton conference?

Jacob

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

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.

-Original Message-
From: CCP4 bulletin board  On Behalf Of Peer Mittl
Sent: Monday, July 22, 2019 6:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Density questionable?

Dear Colleagues,

We are working on a structure where the density for a whole protein chain (>200 
aa) is questionable, since the B-factors exceed 200 Å2 (2.3 Ang resolution). 
However, the initial difference density map and the feature enhanced map 
(normal 2fo-fc map to a minor extend) support the presence of this chain. 
Putting the chain seems equally wrong as not putting it. Putting it reduces 
Rfree by 0.3%. As a conservative researcher I feel tempted to deposit the 
structure without this highly mobile/weakly occupied chain, but other 
researchers may say "he has missed something". Handling this chain like a 
weakly occupied water is probably wrong, but what is the optimal/correct way? 
Is there a general opinion on how the escape this dilemma?

All the best,
Peer



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Density questionable?

[Eleanor Dodson]

Isnt it most likely that this chain is partially occupied?

Eleanor

On Mon, 22 Jul 2019 at 12:32,  wrote:

> Dear Peer,
>
> I did not check, but I expect that atoms with B-factors exceeding 200 Å2
> will not contribute much to the F's at 2.3 Å. A good test might be to
> calculate Rfree's at 4 or 4.5 Å (no refinement!) to see if the missing
> protein chain contributes at low resolution. If it does, I would keep the
> model, if it doesn't, you can consider removing the model.
>
> My 2 cts,
> Herman
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Peer Mittl
> Gesendet: Montag, 22. Juli 2019 12:05
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] [ccp4bb] Density questionable?
>
> EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk
>
>
>
> Dear Colleagues,
>
> We are working on a structure where the density for a whole protein
> chain (>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3
> Ang resolution). However, the initial difference density map and the
> feature enhanced map (normal 2fo-fc map to a minor extend) support the
> presence of this chain. Putting the chain seems equally wrong as not
> putting it. Putting it reduces Rfree by 0.3%. As a conservative
> researcher I feel tempted to deposit the structure without this highly
> mobile/weakly occupied chain, but other researchers may say "he has
> missed something". Handling this chain like a weakly occupied water is
> probably wrong, but what is the optimal/correct way? Is there a general
> opinion on how the escape this dilemma?
>
> All the best,
> Peer
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwID-g=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=O7j1uat8N4jZ5bcK8ivZZRoqkd5rA-z7mp1aFu1o5_I=zNdgTjxGzkcfsoQMY49XR7dq0MCRlmBUJxcD_vWG-y4=
>
> 
>
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[ccp4bb] off topic: job posting

[Artem Evdokimov]

Good morning,

We have two relevant job postingings that I would like to share.

Thank you for your attention :)

Artem

https://careers.massbio.org/job/sr-scientistprincipal-scientist-computational-chemistry/49455467/


and


https://careers.massbio.org/job/scientist-enzymology-protein-chemistry/49690257/

Sr Scientist/Principal Scientist - Computational Chemistry

Enko discovers and develops sustainable solutions for farmers to protect
their crops from pests and disease. It’s proprietary discovery platform
represents a revolutionary approach to rapidly discover novel, safe and
economical solutions that are needed to ensure efficient food production.
Led by a team of proven scientists, entrepreneurs and ag-industry veterans,
Enko uses innovative science and agile design principles to rapidly develop
field-ready crop protection solutions that overcome the rising resistance
barriers traditional pesticides face.

Enko team members will be entitled to participate in Health, Dental,
Vision, Life and Disability insurance, 401(k) plan, and other similar
fringe benefit plans as may be provided by the Company.

We are looking to add a Computational Chemist to join the Chemistry team.
This person will enable the discovery of small molecules for the modulation
of novel biological targets for use in the control of agriculturally
important weeds and pests.

Major responsibilities will include:

Build the computational chemistry project strategy to enhance the
advancement of targets from DNA-encoded library hits to candidate compound
selection
Build the requisite infrastructure to conduct this research, including
identifying tools and technologies needed to support and accelerate
pipeline development and champion their acquisition or the establishment of
collaborations
Lead the structure-based drug design (SBDD) efforts utilizing the suite of
computational chemistry tools including docking/scoring, molecular dynamics
simulations, homology modeling, watermap, and FEP+
Collaborate with medicinal chemists and biologists to create a rich and
diverse pipeline that will address the company’s goals
The ideal candidate will have demonstrated an ability to apply their
expertise in computational chemistry to advance multiple, small molecule
discovery campaigns from screening to development candidates. They will
have demonstrated the ability to thrive in a dynamic, fast-paced,
innovative environment. Excellent written and oral communication skills are
required, as is the desire and ability to excel in a multidisciplinary
environment both as a leader and member across multiple project teams. As
an early addition to the scientific team, this person will have an
opportunity to help us establish a culture that nurtures scientific
excellence, a sense of urgency to achieve project success, and success
built on collaboration and personal accountability.

Qualifications and Skills

D. in Chemistry or a related discipline with 3-5 years of experience in
application of computational chemistry to drug or crop protection chemistry
discovery
Demonstrated expertise in all aspects of modern computational chemistry
including receptor- and structure-based design, conformational analysis,
molecular dynamics, QSAR, binding free energy calculations and
cheminformatics
Track record of accomplishment in small molecule discovery and/or molecular
modelling fields
Demonstration of project leadership and data-driven decision making
Excellent written and oral communication
Strong background in medicinal chemistry, biology, statistics and computer
programming is a plus
No Employment Agencies please, the Company is not responsible for any fees
related to candidates that are unsolicited.

Job Code – PGP13 (Use Job Code in subject line of all communications)

Company: Enko Chem

Contact Name: John Gilroy

Email: john.gil...@enkochem.com

Position Location: Boston, MA

Minimum Required Education: Doctorate

Minimum Years’ Experience: 3-5 years

Scientist, Enzymology & Protein Chemistry

Enko discovers and develops sustainable solutions for farmers to protect
their crops from pests and disease. It’s proprietary discovery platform
represents a revolutionary approach to rapidly discover novel, safe and
economical solutions that are needed to ensure efficient food production.
Led by a team of proven scientists, entrepreneurs and ag-industry veterans,
Enko uses innovative science and agile design principles to rapidly develop
field-ready crop protection solutions that overcome the rising resistance
barriers traditional pesticides face.

Enko team members will be entitled to participate in Health, Dental,
Vision, Life and Disability Insurance, 401(k) Plan and other similar fringe
benefit plans.

We are looking for a creative and highly skilled protein
chemist/enzymologist to join our multidisciplinary team. This scientist
will be responsible for designing, validating, and conducting
enzymatic/biochemical assays and for supporting the overall activities of
the team 

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[David Schuller]

On 7/22/19 3:40 AM, Bärbel Blaum wrote:


"As I said, the lead author may not actually be the crystallographer here"

Bärbel

No need to wonder, that info should be in the PDB file header. The 
author of the coordinates is not necessarily the same as the author of 
the primary reference.



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu




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Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Kay Diederichs]

Proteopedia has this - see 
https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures

Kay

On Fri, 19 Jul 2019 17:42:33 +, Bonsor, Daniel  
wrote:

>Would it be possible to add a public annotations section to the PDB, to allow 
>us to potentially flag/warn whoever downloads that particular structure, there 
>could be something wrong with it, such as wrong space group, no/poor density 
>fitting for ligand. Something similar to PubPeer maybe?
>
>
>Daniel A. Bonsor PhD
>Institute of Human Virology,
>University of Maryland at Baltimore
>725 W. Lombard Street N571
>Baltimore
>MD 21201
>
>
>
>From: CCP4 bulletin board  on behalf of Patrick Loll 
>
>Sent: Friday, July 19, 2019 1:17 PM
>To: CCP4BB@JISCMAIL.AC.UK 
>Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
>
>The idea of contacting the editor (and/or author) is an excellent one, and 
>indeed the correct thing to do scientifically. However, I�m disillusioned: 
>I�ve been down this path before with a high-profile vanity journal, and while 
>the editors paid lip service to the notion that the record should be 
>corrected, in reality they led me on for the better part of a year, and got me 
>to write up detailed analyses of why the ligand positioning was not justified, 
>before eventually saying �no, we don�t see any need to publish a correction.� 
>I speculate that the journal prefers not avoid corrections, for fear that too 
>many corrections will make the journal a less desirable destination.
>
>> On 19 Jul 2019, at 11:23 AM, B�rbel Blaum  
>> wrote:
>>
>> Hi Rhys,
>> the reported B-factors for the �ligands� are all way below the reported 
>> B-factors for the protein chains, with the worst of the three complexes 
>> reporting unitless numbers 23.2 and 64.8, respectively, just to highlight 
>> *one* striking feature of the data collection and refinement table. So even 
>> with the limited info normally available to reviewers this table should have 
>> raised a red flag. After the re-refinement suggested by others, i.e. your 
>> own proper assessment of the crystallographic data, if you do not find 
>> noteworthy density you may want to contact the article�s editor with your 
>> results. If you work in this field, i.e. really care about this paper 
>> scientifically and you are not afraid to confront the authors you could 
>> suggest writing a comment/direct response article but in my opinion that 
>> would only make sense if you can be sure beforehand that it will be linked 
>> visibly to the actual paper, else it will be a waste of time. And don�t 
>> forget that just because one or some of the authors did a bad job at the 
>> crystallographic end other findings of the paper might still be solid � in 
>> collaborations often one author is unable to critically evaluate another 
>> author�s contribution and this would not be the first case were good 
>> synthetic or biological work is presented along with a bad crystal structure.
>> By the way and a bit ironically this protein may have suffered bad 
>> crystallography/scientific practice before - I think it was one of the fake 
>> Krishna Murthy structures, right? The associated (now retracted) article I 
>> mean is here
>> https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub
>[https://ars.els-cdn.com/content/image/S00222836.gif]
>RETRACTED: Crystal structure of dengue virus NS3 protease in complex with a 
>bowman-birk inhibitor: implications for flaviviral polyprotein processing and 
>drug design - ScienceDirect - ScienceDirect.com | Science, health and medical 
>journals, full text articles and 
>books.
>www.sciencedirect.com
>COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center 
>for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA 
>2Department of Biochemistry and Molecular Biology, Kansas University Medical 
>Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue viruses 
>are members of the Flaviviridae and cause dengue fever Dengue fever and dengue 
>hemorrhagic ...
>
>> Kind regards, B�rbel
>> ---
>> B�rbel Blaum, PhD
>> Inthera Bioscience AG
>> Einsiedlerstrasse 34
>> CH-8820 Waedenswil
>> Switzerland
>> E-Mail: baerbel.bl...@intherabio.com
>> Phone: +41 43 477 94 72--
>>
>>
>>
>> Von: CCP4 bulletin board  im Auftrag von "Manfred S. 
>> Weiss" 
>> Antworten an: "Manfred S. Weiss" 
>> Datum: Freitag, 19. Juli 2019 um 16:03
>> An: 
>> Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
>>
>> Hi Rhys,
>>
>> all three structures are at modest resolution and they don't seem to
>> be properly refined. At least they are all below average. I wonder
>> how this paper made it past the referees.
>>
>> I haven't checked the paper, but there are ways and means how to
>> deal 

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[CCP4BB]

Hi John

These are great, but the things that make me suspicious are the values of 
overall R(merge); these are tucked away in the full reports, rather than 
highlighted with all the other structural metrics in the validation sliders. It 
would be wonderful to be able to see at a glance where overall R(merge) values 
like these fit in with those of other deposited structures (even better if it 
could be drawn to the attention of authors before final deposition).

Kay and Gérard have already pointed out that the data processing here may have 
some issues.

Of course, those of us involved in teaching data processing have been 
emphasizing the importance of CC(1/2) rather than relying on R(merge) for 
yonks, but if CC(1/2) isn't given in the report it's all we have to go 

Harry
--
Dr Harry Powell

> On 22 Jul 2019, at 10:05, John Berrisford  wrote:
> 
> Dear Daniel
>  
> The issues you mentioned are highlighted in the wwPDB validation report
> http://www.ebi.ac.uk/pdbe/entry-files/6mo0_full_validation.pdf
> and global issues with the entry are highlighted in the validation sliders
> http://www.ebi.ac.uk/pdbe/entry/pdb/6MO0
>  
> The validation sliders are shown on the entry pages at all wwPDB PDB sites 
> (RCSB, PDBe and PDBj) and they all provide a link to download the wwPDB 
> validation report directly from the entry page.
>  
> Regards
>  
> John
>  
> From: CCP4 bulletin board  On Behalf Of Bonsor, Daniel
> Sent: 19 July 2019 18:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
>  
> Would it be possible to add a public annotations section to the PDB, to allow 
> us to potentially flag/warn whoever downloads that particular structure, 
> there could be something wrong with it, such as wrong space group, no/poor 
> density fitting for ligand. Something similar to PubPeer maybe?
> 
>  
> 
> Daniel A. Bonsor PhD
> Institute of Human Virology,
> University of Maryland at Baltimore
> 725 W. Lombard Street N571
> Baltimore
> MD 21201
>  
> 
> From: CCP4 bulletin board  on behalf of Patrick Loll 
> 
> Sent: Friday, July 19, 2019 1:17 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
>  
> The idea of contacting the editor (and/or author) is an excellent one, and 
> indeed the correct thing to do scientifically. However, I’m disillusioned: 
> I’ve been down this path before with a high-profile vanity journal, and while 
> the editors paid lip service to the notion that the record should be 
> corrected, in reality they led me on for the better part of a year, and got 
> me to write up detailed analyses of why the ligand positioning was not 
> justified, before eventually saying “no, we don’t see any need to publish a 
> correction.” I speculate that the journal prefers not avoid corrections, for 
> fear that too many corrections will make the journal a less desirable 
> destination.
> 
> > On 19 Jul 2019, at 11:23 AM, Bärbel Blaum  
> > wrote:
> > 
> > Hi Rhys,
> > the reported B-factors for the “ligands” are all way below the reported 
> > B-factors for the protein chains, with the worst of the three complexes 
> > reporting unitless numbers 23.2 and 64.8, respectively, just to highlight 
> > *one* striking feature of the data collection and refinement table. So even 
> > with the limited info normally available to reviewers this table should 
> > have raised a red flag. After the re-refinement suggested by others, i.e. 
> > your own proper assessment of the crystallographic data, if you do not find 
> > noteworthy density you may want to contact the article’s editor with your 
> > results. If you work in this field, i.e. really care about this paper 
> > scientifically and you are not afraid to confront the authors you could 
> > suggest writing a comment/direct response article but in my opinion that 
> > would only make sense if you can be sure beforehand that it will be linked 
> > visibly to the actual paper, else it will be a waste of time. And don’t 
> > forget that just because one or some of the authors did a bad job at the 
> > crystallographic end other findings of the paper might still be solid – in 
> > collaborations often one author is unable to critically evaluate another 
> > author’s contribution and this would not be the first case were good 
> > synthetic or biological work is presented along with a bad crystal 
> > structure.
> > By the way and a bit ironically this protein may have suffered bad 
> > crystallography/scientific practice before - I think it was one of the fake 
> > Krishna Murthy structures, right? The associated (now retracted) article I 
> > mean is here
> > https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub
> 
> RETRACTED: Crystal structure of dengue virus NS3 protease in complex with a 
> bowman-birk inhibitor: implications for flaviviral polyprotein processing and 
> drug design - ScienceDirect - ScienceDirect.com | Science, health and 

[ccp4bb] Density questionable?

[Peer Mittl]

Dear Colleagues,

We are working on a structure where the density for a whole protein 
chain (>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3 
Ang resolution). However, the initial difference density map and the 
feature enhanced map (normal 2fo-fc map to a minor extend) support the 
presence of this chain. Putting the chain seems equally wrong as not 
putting it. Putting it reduces Rfree by 0.3%. As a conservative 
researcher I feel tempted to deposit the structure without this highly 
mobile/weakly occupied chain, but other researchers may say "he has 
missed something". Handling this chain like a weakly occupied water is 
probably wrong, but what is the optimal/correct way? Is there a general 
opinion on how the escape this dilemma?


All the best,
Peer



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Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[John Berrisford]

Dear Daniel

 

The issues you mentioned are highlighted in the wwPDB validation report

http://www.ebi.ac.uk/pdbe/entry-files/6mo0_full_validation.pdf

and global issues with the entry are highlighted in the validation sliders

http://www.ebi.ac.uk/pdbe/entry/pdb/6MO0

 

The validation sliders are shown on the entry pages at all wwPDB PDB sites
(RCSB, PDBe and PDBj) and they all provide a link to download the wwPDB
validation report directly from the entry page.

 

Regards

 

John

 

From: CCP4 bulletin board  On Behalf Of Bonsor,
Daniel
Sent: 19 July 2019 18:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Would it be possible to add a public annotations section to the PDB, to
allow us to potentially flag/warn whoever downloads that particular
structure, there could be something wrong with it, such as wrong space
group, no/poor density fitting for ligand. Something similar to PubPeer
maybe? 

 

Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > on behalf of Patrick Loll mailto:pjl...@gmail.com> >
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 

 

The idea of contacting the editor (and/or author) is an excellent one, and
indeed the correct thing to do scientifically. However, I’m disillusioned:
I’ve been down this path before with a high-profile vanity journal, and
while the editors paid lip service to the notion that the record should be
corrected, in reality they led me on for the better part of a year, and got
me to write up detailed analyses of why the ligand positioning was not
justified, before eventually saying “no, we don’t see any need to publish a
correction.” I speculate that the journal prefers not avoid corrections, for
fear that too many corrections will make the journal a less desirable
destination.

> On 19 Jul 2019, at 11:23 AM, Bärbel Blaum mailto:baerbel.bl...@intherabio.com> > wrote:
> 
> Hi Rhys,
> the reported B-factors for the “ligands” are all way below the reported
B-factors for the protein chains, with the worst of the three complexes
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight
*one* striking feature of the data collection and refinement table. So even
with the limited info normally available to reviewers this table should have
raised a red flag. After the re-refinement suggested by others, i.e. your
own proper assessment of the crystallographic data, if you do not find
noteworthy density you may want to contact the article’s editor with your
results. If you work in this field, i.e. really care about this paper
scientifically and you are not afraid to confront the authors you could
suggest writing a comment/direct response article but in my opinion that
would only make sense if you can be sure beforehand that it will be linked
visibly to the actual paper, else it will be a waste of time. And don’t
forget that just because one or some of the authors did a bad job at the
crystallographic end other findings of the paper might still be solid – in
collaborations often one author is unable to critically evaluate another
author’s contribution and this would not be the first case were good
synthetic or biological work is presented along with a bad crystal
structure.
> By the way and a bit ironically this protein may have suffered bad
crystallography/scientific practice before - I think it was one of the fake
Krishna Murthy structures, right? The associated (now retracted) article I
mean is here
>
https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dih
ub 


 
 

 
 RETRACTED: Crystal structure of dengue virus NS3 protease in complex
with a bowman-birk inhibitor: implications for flaviviral polyprotein
processing and drug design - ScienceDirect - ScienceDirect.com | Science,
health and medical journals, full text articles and books.

www.sciencedirect.com  

COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center
for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA
2Department of Biochemistry and Molecular Biology, Kansas University Medical
Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue
viruses are members of the Flaviviridae and cause dengue fever Dengue fever
and dengue hemorrhagic ...


> Kind regards, Bärbel
> ---
> Bärbel Blaum, PhD
> Inthera Bioscience AG
> Einsiedlerstrasse 34
> CH-8820 Waedenswil
> Switzerland
> E-Mail: baerbel.bl...@intherabio.com 

> Phone: +41 43 477 94 72--
>  
>  
>  
> 

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Bärbel Blaum]

You are absolutely right of course, Jacob! I just did that “just for fun”. As I 
said, the lead author may not actually be the crystallographer here and if that 
is the case it is possible that he would actually appreciate some feedback from 
this list. Despite the bad experiences some of us had with editors from glossy 
journals we should not assume bad intentions by all the authors as a group. So 
let’s see what he says.

 

Bärbel

 

-- 

Bärbel Blaum, PhD

Inthera Bioscience AG

Einsiedlerstrasse 34

CH-8820 Waedenswil

Switzerland

E-Mail: baerbel.bl...@intherabio.com

Phone: +41 43 477 94 72--

 

 

 

Von: CCP4 bulletin board  im Auftrag von "Keller, Jacob" 

Antworten an: "Keller, Jacob" 
Datum: Freitag, 19. Juli 2019 um 23:09
An: 
Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

I don’t think anyone mentioned contacting the authors first—doesn’t this seem 
like the first thing one should do?

 

Jacob

 

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

Desk: (571)209-4000 x3159

Cell: (301)592-7004

+

 

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: CCP4 bulletin board  On Behalf Of Roger Rowlett
Sent: Friday, July 19, 2019 4:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

If it is as it appears, it is disappointing to see this in JACS. I would expect 
better. Unfortunately, reviewers don't always get a lot of information to judge 
quality of structures (which has been discussed extensively  on prior occasions 
on this board), so some trust is involved that what data is presented by the 
authors is representative. I see the authors duly presented a 2Fo-Fc map and a 
Fo-Fc omit map in one of the figures, but it appears from a personal 
examination that the Fo-Fc omit map presented may not resemble what one gets 
when personally examining the deposited data, and some protein chain refinement 
problems are immediately evident. That is a bit concerning. High-pressure 
research, coupled with (perhaps) a lack of understanding, experience, and 
supervision is a potentially dangerous ethical stew.

Correcting erroneous published data is challenging. I share the frustration of 
others when attempting to challenge scientifically questionable published 
results. My trip down the rabbit hole (not related directly to crystallography) 
nearly identical to that related previously here. Spend your own time writing a 
full paper rebuttal (ugh) or move on and concentrate resources on your own work.

_
Roger S. Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
email: rrowl...@colgate.edu

On 7/19/2019 2:24 PM, Robbie Joosten wrote:

Even though PDB-REDO cannot salvage this model without extensive rebuilding 
which is what Tristan showed, it is fun to look at the maps and B-factors near 
the ligand. The B-factors go way up and the negative difference density 
disappears, as does most of the 2mFo-DFc density. It’s obviously not news to 
most people on the CCP4BB, properly refining B-factors is really important!

 

Cheers,

Robbie

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bärbel 
Blaum
Sent: Friday, July 19, 2019 17:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Hi Rhys,

the reported B-factors for the “ligands” are all way below the reported 
B-factors for the protein chains, with the worst of the three complexes 
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight *one* 
striking feature of the data collection and refinement table. So even with the 
limited info normally available to reviewers this table should have raised a 
red flag. After the re-refinement suggested by others, i.e. your own proper 
assessment of the crystallographic data, if you do not find noteworthy density 
you may want to contact the article’s editor with your results. If you work in 
this field, i.e. really care about this paper scientifically and you are not 
afraid to confront the authors you could suggest writing a comment/direct 
response article but in my opinion that would only make sense if you can be 
sure beforehand that it will be linked visibly to the actual paper, else it 
will be a waste of time. And don’t forget that just because one or some of the 
authors did a bad job at the crystallographic end other findings of the paper 
might still be 

Re: [ccp4bb] challenges in structural biology

[Kay Diederichs]

Dear Artem, Tom, Janet,

for me and probably others the usage of words like 'magic bullet' (which you 
defend, or try to redefine) implies a belief-based esoteric approach that has 
little to do with science. I suggest that to obtain funding, 'magic bullets' 
should not be promised, because these cannot be delivered  (I gave the 
lo-gravity hi-funding example). 

That this discussion (including messages by Janet and Tom) happens at all 
suggests that crystallization is currently not a science - it lacks a 
consistent nomenclature and way of documentation, and suffers from strong 
publication bias (many unpublished negative results).

On the other hand, what you (Janet, Tom) write about the research that 
should/could be performed - this sounds a lot like a scientific approach, and 
is not different from what has been realized in other areas of crystallography. 
Yes, existing tools for predicting crystallization success are not consulted 
because the rate of false positives and false negatives is high. If those rates 
could be reproducibly reduced, I bet the usage would go up - that could start a 
feedback loop leading to even better predictions. Is work in this direction 
sexy? No. Is it useful? Yes. Is it hard work? Yes. Does it contribute to make 
crystallization a science? Yes.

What about 'deep learning' applied to crystallization outcomes? Can it guide 
individual trials better than intuition? Can it find previously unknown 
promising combinations on a larger scale?

Can this be funded? Yes of course. Your statement that crystallization gets no 
funding may be true in some countries (but aren't CCP4BB readers from the U.S. 
also reviewers?), but it's untrue in others - think of groups in France that 
obviously got long-term funding. And for space (low-gravity) - that amount of 
funding could have been used for a lot of meaningful earth-bound research.

Kay


Am 21.07.19 um 23:04 schrieb Artem Evdokimov:
> Dear Kay
>  
> 
> I disagree that 'magic bullet' is impossible. I think the definition is wrong 
> here - magic bullet to me is a rational set of methods that (when executed 
> with precision and care) enable crystallization to the maximum possible 
> benefit. This includes everything - constructs, crystallization design, etc. 
> Part of the magic bullet is also a precise knowledge when crystallization is 
> unlikely (i.e. an actual proven predictor that consistently discriminates 
> between "you're going to succeed if you work hard" and "it's doomed to fail, 
> don't bother" scenarios in crystallization.
> 
> The above is not sexy. It does not present itself as a lovely subject on 
> which to have international cocktail parties with politicians delivering 
> fancy speeches. But that is what is needed, and no one is funding that to the 
> best of my knowledge.
> 
> What needs to be done is a significant amount of testing, standardization, 
> and methods development from the perspective of holistic outcome (i.e. 
> crystals that work) - and none of the previously advertised 'magic bullets' 
> work the way I just described.
> 
> Having written this, I think you're right - this is a bit of a distraction 
> from James' original point. However it's a valid opportunity for a lively 
> discussion on its own :)
> 
> Artem
> 
> - Cosmic Cats approve of this message
> 
> 
> On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> 
> wrote:
> 
> Dear Artem,
> 
> black or white is not my way of thinking, which is why I don't believe in 
> Hannibal's approach when it comes to crystallization.
> 
> None of the magic bullets that were advertised over the past decades have 
> proven generally applicable.  I believe more in incremental improvement which 
> in this case includes a few biophysical characterization methods, possibly 
> improved microfluidics or other apparatus, and expanded screens. And a lot of 
> hard work, perseverance, intuition, frustration
>  tolerance. Nothing that really needs huge funding - of course it does 
> need money, but just a  share of what is anyway needed for the usual lab work 
> including expression, purification, functional characterization, binding 
> studies and the like.
> 
> One area where a huge amount of money was burnt is crystallization in 
> space, on board of e.g. the spacelab and ISS. This is for me an example of a 
> mis-led approach to throw money at a difficult problem, with the expectation 
> of a solution. Science does not work like that, and money in this case seems 
> more to be the problem than the solution.
> 
> This example may illustrate a certain failure of us scientists to resist 
> the temptation to promise unrealistic outcomes when confronted with money 
> provided for political reasons, which ultimately undermines our credibility. 
> But this takes us away from James' points.
> 
> best,
> 
> Kay
> 
> On Sun, 21 Jul 2019 16:06:48 -0400, Artem Evdokimov 
>