Re: [ccp4bb] About the A in AI

[DUMAS Philippe (IGBMC)]

Bayesian reasoning: Given the observation of the complete identity of the 2 
reports, what is the likelyhood that Bing & ChatGPT arrived at the same result 
vs. the null hypothesis that Bernhard made a simple "cut & paste" mistake. 


Philippe Dumas 


De: "Bruno KLAHOLZ"  
À: "CCP4BB"  
Envoyé: Vendredi 12 Mai 2023 17:35:40 
Objet: Re: [ccp4bb] About the A in AI 





indeed, probably they are using the same databases and features. 

Same happens in translations btw. 



Cheers, 



Bruno 





From: CCP4 bulletin board  On Behalf Of Ian Tickle 
Sent: 12 May 2023 17:33 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] About the A in AI 







Hi Bernhard 





Methinks there's some cribbing going on between Bing and ChatGPT - not only 
deja-vu but the reviews are identical word for word! How is that possible? 





Cheers 





-- Ian 








On Fri, 12 May 2023 at 16:15, Bernhard Rupp < [ mailto:hofkristall...@gmail.com 
| hofkristall...@gmail.com ] > wrote: 





For those who concern themselves with such matters, here the responses from 
Bing and ChatGPT to the prompt: 



“Please write a critical review report rejecting a scientific paper reporting 
that the 1.0 angstrom crystal structure shows that psiX is a trimethylating 
enzyme” 



Enjoy the frightening reading and then we can chat (LOL) about the creepy 
feeling of déjà-vu you might experience…. 



[ https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0 | 
https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0 ] 

[ https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0 | 
https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0 ] 



Cheers, BR 



- 
Bernhard Rupp 

k.k. Hofkristallamt 

001 (925) 209-7429 
+43 (676) 571-0536 
[ mailto:b...@ruppweb.org | b...@ruppweb.org ] 
[ mailto:hofkristall...@gmail.com | hofkristall...@gmail.com ] 
[ http://www.hofkristallamt.org/ | http://www.hofkristallamt.org/ ] 
- 
Hope is not a strategy - hope is a mistake. 

- 








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Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

[DUMAS Philippe (IGBMC)]

It seems to me that it is legitimate to refer to what you describe as 
"twinning". That's the difference between merohedral and non-merohedral 
twinning. What you describe is non-merohedral twinning. 
In fact twinning has been (re)discovered by most of the biological community 
after the remarkable article by T.O. Yeates in Methods in Enz. (1997) vol 276A 
pp. 344-358. Only after this reminder did papers in biocrystallography mention 
twinning currently. (I can refer to my own experience because the Yeates' paper 
allowed us (1) to discover the problem of twinning and (2) to solve a twinned 
structure). Probably, your feeling comes from the fact that structural 
biologists were only concerned by solving their structure and never considered 
multiple crystals (non-merohedral twinning) as a real problem, but only as a 
practical problem, since everyone knew that such crystals had to be either let 
aside or broken into single crystals. 
However, twinning has always been extremely well know in mineralogy because it 
is extremely common to see natural crystals showing non-merohedral twinning. 
And mineralogists commonly have long described crystal habits by twinning 
observed with crystals of specific molecules. 

I suggest that you ask google for "macle rutile wurtzite quartz" (macle is 
twinning in French) and you select images. All these photographs are for 
twinned crystals. All of that was extremely well described in a venerable book 
by Friedel in 1911 when none of us was born. 

I think all of that is not just pure semantics. Am I wrong ? 

Philippe Dumas 



De: "Ana Luísa Moreira de Carvalho"  
À: "CCP4BB"  
Envoyé: Mercredi 17 Mars 2021 11:12:53 
Objet: Re: [ccp4bb] Can twinning be seen in the diffraction pattern? 

Just a short note on this: I often see colleagues using the word “twinning" 
when referring to a crystal that is actually multiple (not single). 

I think much confusion arises from this. For me, a twin crystal is the one that 
looks single under the microscope and only intensity statistics reveal that the 
diffraction comes from more than one crystal. 

If a crystal looks multiple, i do not call it a twin. Am i being too meticulous 
on this? 
Thanks! 




On 16 Mar 2021, at 13:31, Eleanor Dodson < [ 
mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk | 
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk ] > wrote: 

You usually detect twinning most reliably from the intensity statistics - 
CCP4I2 and Xtriage report those.. 
Eleanor 

On Tue, 16 Mar 2021 at 07:31, Marina Gárdonyi < [ 
mailto:marina@pharmazie.uni-marburg.de | 
marina@pharmazie.uni-marburg.de ] > wrote: 

BQ_BEGIN
Dear all, 

thanks to all who helped me solving the question. You sent me a lot of 
comments and information I have not taken into account. 
After reading all the answers, I have come to the conclusion that the 
spots that are very close to each other come from the long cell axis 
(57-57-160) and that twinning can probably not be seen in my case. I 
should have mentioned that the diffraction images came from an 
in-house x-ray machine, recorded with a 0.5 degree rotation range. 

Thank you all again! 

Kind regards, 
Marina 

-- 
Marina Gárdonyi 

PhD Student, Research Group Professor Dr. Klebe 

Department of Pharmaceutical Chemistry 

Philipps-University Marburg 

Marbacher Weg 6, 35032 Marburg, Germany 

Phone: +49 6421 28 21392 

E-Mail: [ mailto:marina@pharmazie.uni-marburg.de | 
marina@pharmazie.uni-marburg.de ] 

[ http://www.agklebe.de/ | http://www.agklebe.de/ ] 

 

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Re: [ccp4bb] Regarding difference in ITC and structure data

[DUMAS Philippe (IGBMC)]

Monika 
Did you try ITC experiments at different temperatures ? 
Delta H may be null, or close to zero, at some temperature without implying 
that there is no binding ! 
Philippe Dumas 


De: "monika chandravanshi"  
À: "CCP4BB"  
Envoyé: Samedi 1 Août 2020 09:57:24 
Objet: [ccp4bb] Regarding difference in ITC and structure data 



Dear All, 

I am working on a carbohydrate-binding protein, which co-crystallizes with 
maltose, maltotriose, maltotetraose and maltopentaose and the same can be 
supported by ITC experiments as well. Also, the mutant protein (X2Y) 
co-crystallizes with maltose, maltotriose, maltotetraose and maltopentaose, 
however, the binding of only maltotriose and maltotetraose could be observed 
through ITC. For your information, the ITC conditions are the same for all the 
ligands and the ligand concentration used in ITC is same as used in 
crystallization (100x of protein concentrations). Moreover, from structural 
analysis, we have observed that the binding mode of all ligands is the same. 

I request your suggestion on why maltose and maltopentaose do not show any 
binding to the mutant protein in ITC experiments. 

Looking forward to suggestions. 

Best Regards, 
Monika 




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Re: [ccp4bb] disinfecting keyboards

[DUMAS Philippe (IGBMC)]

I got a good advice about it: inject WhiteHouse disinfectant right into the cpu.
Good to repeat it a couple of times, but wear mask and gloves against possible 
Cotrump-16-20 last attacks !
Hope it will be helpful.
Philippe Dumas 
(#SupportFauci)



- Mail original -
De: "Jurgen Bosch" 
À: "CCP4BB" 
Envoyé: Mercredi 29 Avril 2020 21:35:06
Objet: Re: [ccp4bb] disinfecting keyboards

You really just need two keyboards per computer, every user change, just add 
the used keyboards into the hutch, the rest should take care of itself then.

You are at the source to successfully blast these little viruses

Jürgen 
> On Apr 29, 2020, at 3:30 PM, James Holton  wrote:
> 
> Keyboards are cheap.  Why not everyone get their own?
> 
> Then we can all stop fighting about whether the  key should be shaped 
> like an "L" or not.
> 
> -James Holton
> MAD Scientist
> 
> On 4/29/2020 11:53 AM, Tim Gruene wrote:
>> Dear all,
>> 
>> can you make suggestions for how to disinfect computer keyboards, and
>> instrument panels?
>> 
>> Our facility is going to reboot next week, with shifts so that people
>> don't meet. The main interface will be the computer keyboards, as well
>> as the door of our X-ray diffractometer and the mounting of the
>> crystals.
>> 
>> The keyboard labels may not like alcohols (and the efficiency of
>> injecting disinfecting through the USB cable is also under discussion,
>> so I heard).
>> 
>> One way would be to use individual keyboards, and wearing gloves for
>> replugging, and to use gloves for mounting crystals.
>> 
>> But maybe there are other ways that won't require gloves?
>> 
>> Best regards,
>> Tim
>> 
> 
> 
> 
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Re: [ccp4bb] CCP4BB vs COVID19

[DUMAS Philippe (IGBMC)]

Relevant to the discussion: 

* Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press 
An RNA Thermosensor Controls Expression of Virulence Genes in Listeria 
monocytogenes 

* Bacterial RNA thermometers: molecular zippers and switches 
Jens Kortmann and Franz Narberhaus 
NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255 

*An RNA Thermometer Activity of the West Nile Virus Genomic 30-Terminal 
Stem-Loop Element Modulates Viral Replication Eciency during Host Switching 
Viruses 2020, 12, 104; doi:10.3390/v12010104 

* Temperature triggers immune evasion by Neisseria meningitidis 
Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget 
Gollan2, Helen Ewles2, Ronald Chalmers3, 
Vladimir Pelicic2 & Christoph M. Tang1,2 
Nature (2013) 

Philippe Dumas 

De: "James Holton"  
À: "CCP4BB"  
Envoyé: Dimanche 22 Mars 2020 16:38:28 
Objet: Re: [ccp4bb] CCP4BB vs COVID19 

Thank you Patrick, 

RNA structure is still structural biology, so I think relevant here. It seems 
to me that RNA as a thermometer would be an easy hypothesis to test? Has anyone 
measured virulence vs temperature in cell culture? 

The 3D structure of the genome is no doublt important. I wouldn't want to try 
crystallizing the whole thing, but I wonder if this might be an excellent 
target for cryoEM? A challenge for that "we can classify our way out of 
anything" philosophy? And the result would most certainly be interesting. 

-James Holton 
MAD Scientist 

On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote: 




James, this isn't conventional structural biology, but may be of interest, and 
I haven't been able get any mainstream virologists to think about it. 

The protein sequences are obviously of interest, but so are the RNA sequences 
at both ends of the Covid genome, which have conserved secondary structure. A 
few years ago a paper came out suggesting that wild-type influenza has multiple 
"RNA thermometers", which may play an important role in the tropism of 
influenza. Similar mechanisms may exist in other respiratory viruses, including 
Covid. 

My take on this, and the relevant papers, are below. 

Good luck to everyone and stay well, 

Patrick 



BQ_BEGIN

[ 
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
 | 
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
 ] 

My paper in Medical Hypotheses [ 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf | 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf ] 

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA 
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16. 

Chursov, Andrey, et al. "Specific temperature-induced perturbations of 
secondary mRNA structures are associated with the cold-adapted 
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 
1266-1274. 

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of 
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133. 





On Fri, Mar 20, 2020 at 10:59 PM James Holton < [ mailto:jmhol...@lbl.gov | 
jmhol...@lbl.gov ] > wrote: 

BQ_BEGIN
You might think that as a structural biologist you won't be able to do 
much about COVID-19 anytime soon, but that is not true. Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how 
fast we can get started. There are 21 PDBs already and some even have 
bound ligands. Good job Frank et al. BTW! And my personal thanks to 
all of you out there who are already hard at work on this. 

I believe this forum is an ideal place to share information and ideas on 
the structural biology of SARS-CoV-2 as we move forward. It's a big 
virus, but there are not that many proteins in it. If all of us 
independently do the same bioinformatics and literature searches and end 
up trying exactly the same thing in every lab all over the world, then 
that would be more than unfortunate. To that end, I am personally 
interested on ORF8 for reasons I will go into below. Has anyone tried 
to solve it yet? What happened? Didn't express? Bad diffraction? 
What? Do tell. 

Some of us, as you may have heard, are stuck at home, our beamlines and 
labs dark while we shelter-in-place. That doesn't mean our hands are 
tied. We are still allowed to think. The fraction of the human race 
that has a snowball's chance in Hades of figuring out this bug is very 
very small. Structure may be your main skill set, but you are still a 
biologist. Do you know how to run a PCR machine? Do you know how to 
pipette? You might think that anybody can do it, but that is really not 
the case. Ever trained a new student on sterile technique? How many 
days did that take? Now remember that your student was no dummy and 
already studying biology. Everyone reading this will make an excellent 
volenteer at the very least. I'm not saying this to belittle the 
average human, only to say that we scientists, moving in 

Re: [ccp4bb] ITC Stoichiometry

[DUMAS Philippe (IGBMC)]

Dear Angshu 
The answer to your question requires to define precisely the term of 
"stoichiometry". 
*If you consider the hexamer as "the molecule B", then the expected 
stoichiometric ratio is 1/1 (one molecule A should bind to 1 hexamer B). 
*But if you consider the monomer of B as "the molecule" in the cell, then the 
expected stoichiometric ratio is 1/6 (one molecule of A should bind to 6 
monomers of the hexamer B). 
Accordingly, you have to define the concentration in the cell as follows: if 
you consider the hexamer as "the molecule B" and, let's suppose you have [B] = 
10 µM of hexamer, then [B] = 60 µM if you consider the monomer of B as "the 
molecule". 
I hope I answered your question. 
Philippe Dumas 


De: "Angshu Dutta"  
À: "CCP4BB"  
Envoyé: Vendredi 21 Février 2020 15:24:53 
Objet: [ccp4bb] ITC Stoichiometry 



Dear all, 

Apologies for an off-topic question. 


There are two proteins- A(monomer) and B(hexamer). As per reports, one molecule 
of A(monomer) should bind to one molecule of B(hexamer). In order to show the 
interaction between the two proteins through ITC, A is taken in the syringe and 
B is taken in the cell. What kind of stoichiometry values should be expected? 

I look forward to your responses. 

Many thanks in advance. 

Best, 

Angshu 




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Re: [ccp4bb] ITC question -dimer vs monomer

[DUMAS Philippe (IGBMC)]

Dear Bernhard 
I share your intuition: we should expect to observe different shapes of 
titration curves depending on whether A or B2 is in the syringe (titration and 
reverse titration). 
I suppose that you want to test your hypothesis that, eventually, you get A2B2. 
Independently of any kinetic considerations , one should consider the 
possibility that the successive equilibria A+B2<-->AB2 and A + AB2 <-->A2B2 
have distinct Kds and distinct DeltaH (which would of course be more favorable 
to detect these two distinct binding events, if they exist). 
I therefore suggest that you perform both possible titrations (if each protein 
can be sufficiently concentrated to be in the syringe) and that you try to fit 
each titration curve with the same model of interaction. If this works well, 
then the must would be to fit both titration curves at the same time with the 
same model of interaction . This is certainly the most demanding method to test 
a hypothesis and this is not at all equivalent to fit independently the two 
kinds of titration curves as you can imagine. (Let's say that this would amount 
to refine a single molecular model against crystal data from two space 
groups).The problem is of the practical possibility of doing such a joint fit 
with the available programs. I personally do such things with my own (not 
user-friendly!) programs. As far a I know, this is not possible, neither with 
Origin or PEAQ from Malvern, nor with NanoAnalyze from TA. I know that 
AFFINImeter is quite flexible to allow using specific models, but I'm not sure 
it would allow you to make such a global fit. I don't know about the 
possibility of SEDPHAT developed by P. Schuck. 
I hope this fits with your expectations. 
Best 
Philippe Dumas 



De: "Bernhard Rupp"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Jeudi 3 Octobre 2019 17:05:56 
Objet: [ccp4bb] ITC question -dimer vs monomer 



Hi Fellows, 



please let me ask the respective experts an ITC question: I have 2 proteins, 
stable and dialyzed in identical buffer. 

A is a monomer and B an obligate dimer. I suspect that eventually a A2B2 dimer 
will form. 



Intuitively, it should make a difference whether I titrate the dimer with the 
monomer or vice versa. 

In the first case, a momomer would initially meet a lot of free dimers, and I 
would expect that randomly, a AB2 complex 

is more likely to form than a A2B2 (let’s disregard any more complex 
colligative/cooperative effects). 



If I drip the dimer into the monomer pool, it is quite likely that the B dimer 
meets 2 free As, and I get right away a higher population of A2B2s. 



Maybe at dilutions of ITC and with sufficient equilibration that is not an 
issue at all (again, absent any cooperative effects that might alter the first 
Kd vs. the second, despite the sites on the dimer are at least initially 
equivalent). 



Can someone guide me towards literature about this or perhaps share some 
first-hand experience? 



Many thanks, BR 



-- 

Bernhard Rupp 

[ http://www.hofkristallamt.org/ | http://www.hofkristallamt.org/ ] 

[ mailto:b...@hofkristallamt.org | b...@hofkristallamt.org ] 

+1 925 209 7429 

+43 676 571 0536 

-- 

Many plausible ideas vanish 

at the presence of thought 

-- 






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Re: [ccp4bb] Interesting pattern on a crystallization drop

[IGBMC]

Le Jeudi 28 Mars 2019 12:03 CET, jai mohan 
<0cab66323371-dmarc-requ...@jiscmail.ac.uk> a écrit:

A friend of mine (Angel Piñeiro) just suggested to me the "Maragoni effect", 
which is likely active in the dancing droplets from Stanford and might explain 
the "explosion" into separate bubbles
Indeed, one can see on Wikipedia a video illustrating how the contact of fluids 
with different surface tensions can have big effects...


>  May be, I do co-relate your crystal pic with Manu Prakash at Stanford on his 
> work on Dancing Droplets, briefing the surface tension and evaporation ^ the 
> rule of two component fluids. # Since your precipitant contain PVP a shape 
> controlling agent 
> #https://med.stanford.edu/news/all-news/2015/03/researchers-solve-mystery-of-the-dancing-droplets.html
>
> Best wishes
> S.M.Jaimohan PhD
> On Thursday, 28 March, 2019, 1:54:23 pm IST, Sergei Strelkov 
>  wrote:
>
>  #yiv3861306982 #yiv3861306982 
> --P{margin-top:0;margin-bottom:0;}#yiv3861306982
> Artem (and Beatriz),
>
>
>
>
>
> Me bad, could have thought about that! I think you are right.
>
>
>
>
> There were initially bubbles in each drop (7 in one case, 4 in the other).
>
> At some point the bubbles exploded (it was an instantaneous process, not just 
> shrinking).
>
>
>
>
> Kind regards,
>
> Sergei
>
>
>
>
> Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
> Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 
> bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 
> 32 Lab pages: http://pharm.kuleuven.be/BiocrystallographyFrom: CCP4 bulletin 
> board  on behalf of Artem Evdokimov 
> 
> Sent: Thursday, March 28, 2019 1:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Interesting pattern on a crystallization drop Neat!
> Looks like multiple adjacent bubbles that were initially touching but 
> eventually shrunk down to the central cores - the connectors are protein 
> filaments (skin on the bubbles) left over from when bubbles had contact 
> points.
> Artem
> On Wed, Mar 27, 2019, 19:39 Marshall, Bevan (Manufacturing, Parkville) 
>  wrote:
>
>
> Looked up the condition on C6 (https://c6.csiro.au/C6.asp) and that condition 
> is found in both Index and JCSG screens as well as Classics II.
>
>  
>
>  
>
> Bevan Marshall
> Staff Scientist | Collaborative Crystallisation Centre
> Manufacturing
> CSIRO
>
> E bevan.marsh...@csiro.aut +61 3 9662 7492 
> 343-351 Royal Parade, Parkville, VIC 3052
> www.csiro.au|https://c3.csiro.au 
> CSIRO acknowledges the Traditional Owners of the lands that we live and work 
> on across Australia and pays its respect to Elders past and present.
>
> PLEASE NOTE
> The information contained in this email may be confidential or privileged. 
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> warrant and/or guarantee that the integrity of this communication has been 
> maintained or that the communication is free of errors, virus, interception 
> or interference.
>
> Please consider the environment before printing this email.
>
>  
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of LEGRAND 
> Pierre
> Sent: Thursday, 28 March 2019 9:13 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Interesting pattern on a crystallization drop
>
>  
>
> Dear Beatriz,
>
>  
>
> Nice drops :-))
>
> Could it be that there is a reaction going on in these drops ?
>
> The conditions are quite "exotic" with possibilities of coordination or 
> oxydoreduction (Co2+/Co3+) or polymerization...
>
> Do you have reductants with the protein buffer ?
>
> Is the protein an enzyme or a metalloprotein ?
>
> Just some ideas.
>
>  
>
> Best wishes,
>
> Pierre
>
>  
>
> De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Beatriz Gomes 
> Guimaraes [beatriz.guimar...@fiocruz.br]
> Envoyé : mercredi 27 mars 2019 19:44
> À : CCP4BB@JISCMAIL.AC.UK
> Objet : [ccp4bb] Interesting pattern on a crystallization drop
>
> Dear all,
>
>  
>
> I would like to share with you a surprising pattern I found when examining 
> some crystallization plates (attached figures).
>
>  
>
> It is less obvious looking the photos, but apparently the "lines" are formed 
> by precipitated protein and there are some "bubbles" with small drops 
> inside.I wish they were microcrystals but I do not think this is the case.
>
> I was suprised by the symmetry !
>
>  
>
> And it is not completely random because for the same condition the difference 
> between the two drops are : protein alone ("hexagon") and protein + ligand 
> ("rhombus")
>
>  
>
> crystallization condition is:
>
> 0.01 M Cobalt(II) chloride hexahydrate
>
> 0.1 M Tris pH 8.5
>
> 20% w/v Polyvinylpyrrolidone K 15
>
>  
>
> Have you seen anything similar before?
>
>  
>
> Thank you for your 

Re: [ccp4bb] Interesting pattern on a crystallization drop

[IGBMC]

Le Mercredi 27 Mars 2019 19:44 CET, Beatriz Gomes Guimaraes 
 a écrit:

In four days from now, I (everyone) would have taken this as a Photoshop joke...
Quite amazing! Is it reproducible?
What is the protein? Tubulin ? ::))
Philippe Dumas


> Dear all,
>
>
> I would like to share with you a surprising pattern I found when examining 
> some crystallization plates (attached figures).
>
>
> It is less obvious looking the photos, but apparently the "lines" are formed 
> by precipitated protein and there are some "bubbles" with small drops inside. 
> I wish they were microcrystals but I do not think this is the case.
>
> I was suprised by the symmetry !
>
>
> And it is not completely random because for the same condition the difference 
> between the two drops are : protein alone ("hexagon") and protein + ligand 
> ("rhombus")
>
>
> crystallization condition is:
>
> 0.01 M Cobalt(II) chloride hexahydrate
>
> 0.1 M Tris pH 8.5
>
> 20% w/v Polyvinylpyrrolidone K 15
>
>
> Have you seen anything similar before?
>
>
> Thank you for your comments!
>
> Beatriz
>
>
>
> --
> Beatriz Guimarães
> Laboratory of Structural Biology and Protein Engineering
> Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
> Rua Prof. Algacyr Munhoz Mader, 3775   Bloco C
> CIC 81350-010
> Curitiba - PR, Brasil
> Tel.:+55(41)3316-3225/2104-3438
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1







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Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[IGBMC]

Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud  a écrit:

Dale
Good to have the opportunity of going back to the crystallography of the 
fifties in these post-modern times...
There is an essential argumentation that should be recalled. The only reason 
for the fact that one ignores low-resolution data in a Wilson plot is that a 
Wilson plot is based precisely upon Wilson statistics, which assumes that the 
atoms are cast randomly in the unit cell.
This assumption obviously does not hold at low resolution and there is no 
reason to obtain a straight line that stems from the latter assumption.
Therefore, I do not think one may say that a Wilson plot tends to ignore atoms 
with high B values.
Consequence: if one has data at rather low resolution, a Wilson plot is 
inherently inaccurate, but if one has data at very high resolution, the Wilson 
plot should give a very decent estimate of the average B and any significant 
discrepancy should ring the bell.
Philippe Dumas


>The numeric average of the B factors of the atoms in your model only
> roughly corresponds to the calculation of the Wilson B.  While I always
> expect the average B to be larger than the Wilson B, how much larger

> depends on many factors, making it a fairly useless criteria for judging
> the correctness of a model.
>
>While it is pretty easy to understand the average of the B factors in
> your model, the Wilson B is more difficult.  Since it is calculated by
> drawing a line though the (Log of) the intensity of your structure
> factors as a function of the square of sin theta over lambda, it is
> rather removed from the atomic B factors.  When drawing the line the low
> resolution data are ignored because those data don't fall on a straight
> line, and this means that the large B factor atoms in your model are

> ignored in the Wilson B calculation.
>
>The Wilson B is (sort of) a weighted average of the B factors of your
> model, with the smallest B's given the largest weight.  The actually

> weighting factor is a little obscure so I don't know how to simulate it
> to adjust the averaging of atomic B's to come out a match.  The easiest
> way to compare your model to the Wilson B is to calculate structure
> factors from it and calculate the Calculated Wilson B.  No one does this
> because it will always come out as a match.  If your calculated Wilson B
> doesn't match the observed Wilson B your R values are guaranteed to be
> unacceptable and your refinement program will have to be malfunctioning
> to create such a model.
>
>If all the B factors in your model are equal to each other, your
> refined model will have an average B that matches the Wilson B, because
> weighting doesn't matter in that situation.  If you allow the B's to

> vary, the difference between the average and the Wilson B will depend on
> how high of an individual B factor you are willing to tolerate.  If you
> are a person who likes to build chain into weak loops of density, or

> build side chains where there is little to no density, then your average
> B will be much larger than the Wilson B.  This does not mean there is an
> error, it is simply a reflection of the Wilson B's insensitivity to
> atoms with large B.
>
>I do not believe comparing the average B to the Wilson B has any
> utility at all.
>
> Dale Tronrud
>
> On 3/12/2019 11:34 AM, Eze Chivi wrote:
> > Dear CCP4bb community,
> >
> >
> > The average B-factor (calculated from model) of my protein is 65,
> > whereas the Wilson B is 52. I have read in this BB that "it is expected
> > that average B does not deviate strongly from the Wilson B". How I can
> > evaluate if the difference calculated for my data is razonable or not?
> >
> >
> > Thank you in advance
> >
> >
> > Ezequiel
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
> 
>
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Re: [ccp4bb] Purchasing slides with diffraction gratings for teaching diffraction

[IGBMC]

Le Mardi 5 Mars 2019 10:41 CET, "Roversi, Pietro (Dr.)"  
a écrit:

Many years ago I did teaching on diffraction by illustrating the major aspects 
of crystal structure determination with 2D crystals on 24x36 films. The crystal 
was an 80x60 repeats of the famous Einstein's tongue and MIR was illustrated 
with "beauty spots" added on Einstein's face. You can have a look to the 
attached diffraction image and  to the little article in the IUCr newsletter on 
teaching, June 2006:

https://www.iucr.org/resources/commissions/crystallographic-teaching/newsletters/1

Two remarks:
First, unfortunately, the web site indicated in the article is essentially 
"dead" (but not completely) due to license problems with WebMathematica.
Second, it is mentioned in the article that Friedel's law was significantly 
violated and that this was due to bad alignment of the negative film in the 
optical diffractometer. I'm no more sure that this is exact and I am wondering 
whether this could be due to a much more interesting effect of "anomalous 
diffraction" due to different optic lengths within the negative resulting from 
different amounts of reduced silver. (Does anyone has an idea about that?). If 
this were true, then on could imagine solving the Einstein's crystal structure, 
not only by MIR as shown initially, but also by SAD, and this would be very 
interesting. I long thought that I should come back to this teaching problem, 
but I never did it. Who knows: someone else could be interested...

I would be very glad of sending you some "2D Einstein's tongue crystals" for 
your teaching.

All the best
Philippe Dumas



> Dear all,
>
> I'd like to purchase slides with diffraction gratings for educational 
> purposes.
>
> Ideally, to be used with a visible-light laser pointer.
>
> And: with 1D and 2D patterns, of variable repeats - so as to be able to 
> illustrate the effect on the spacing in reciprocal space, as it were.
>
> I am looking online but not having much joy.
>
> Can anyone recommend a good provider to purchase from?
>
> Thank you!
>
> Pietro
>
>
>
> Pietro Roversi
>
> LISCB Wellcome Trust ISSF Fellow
>
> https://bit.ly/2I4Wm5Z
>
>
> Leicester Institute of Structural and Chemical Biology
> Department of Molecular and Cell Biology, University of Leicester
> Henry Wellcome Building
> Lancaster Road, Leicester, LE1 7HB
> England, United Kingdom
>
> Tel. +44 (0)116 2297237
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1








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DiffractionEisteinTongue.pdf
Description: Adobe PDF document

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning

[IGBMC]

Le Vendredi 11 Janvier 2019 12:18 CET,  a écrit:

Thank you Herman you for this clear and informative comments !!
Particularly your last point, which I found very instructive.
Now I remember the title of the article by T.O. Yeates "Protein crystals and 
their evil twins" in 1999. And this corresponds well to the difficulty of the 
problem.
Philippe D.

Philippe Dumas

> Dear Philippe,
>
> As Randy just pointed out, when twinning, pseudosymmetry and other 
> pathologies come into play, things really get complicated.
> I agree with what you said but for the current problem, things may be more 
> complicated.
>
> To summarize:
> - "bona fide" twinning: there are two different, intergrown crystals and the 
> intensities of both crystals just add up.
> - "nano scale" twinning, called statistical disorder: the two orientations 
> are randomly distributed through the crystals and the diffraction of both 
> conformations interferes. The conformations behave like alternate 
> conformations.
> - Twinning/pseudosymmetry/wrong unit cell etc.: Here the two conformations, 
> present in the large (true) unit cell and related by crystallographic or 
> noncrystallographic symmetry, may not fit in the small (false) unit cell and 
> be accounted for by introducing twinning where none is present. Especially 
> with 6 twinning operators, the refinement programs have a lot of room to 
> tweak around to reduce the R-factors.
>
> Therefore my advice would be:
> - Critically check the space group and especially how weak are the weak 
> reflections discarded with the small unit cell?
> - the solution you got in the small unit cell may be a subset of what is 
> present in the large unit cell, so I would also try molecular replacement 
> with the ensemble of molecules you got in the small unit cell.
>
> My two cents,
> Herman
>
>
> -Ursprüngliche Nachricht-
> Von: DUMAS Philippe (IGBMC) [mailto:p.du...@ibmc-cnrs.unistra.fr]
> Gesendet: Freitag, 11. Januar 2019 11:52
> An: Schreuder, Herman /DE
> Cc: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS 
> & twinning
>
>
> Le Vendredi 11 Janvier 2019 09:07 CET, herman.schreu...@sanofi.com a écrit:
>
> Dear Herman,
> As far as I understood the twinning problem, what you say is only true in 
> some occasions, and not in others.
> If the "macroscopic" domains are so small that they are smaller than the 
> X-rays coherence length, then you may do what you say because the X-rays 
> emitted by the different domains can interfere.
> But, if the domains become large, the X-rays emitted by the different domains 
> do not interfere anymore and you have to add the weighted intensities, not 
> the amplitudes, of each domain.
> I hope I understood well your comment and did not "interfere negatively" with 
> the thread...
> Best
> Philippe Dumas
>
> > Dear Lan,
> >
> > Thank you for your compliment. I do not use Xtriage, so I did not bother 
> > looking at the log files.
> >
> > What I meant to say is that with twinning, the crystal has different 
> > macroscopic domains where the molecules have different orientations, say 
> > one domain with orientation A and one domain with orientation B. Since 
> > these domains grow on top of each other, they are usually related by a twin 
> > operator similar to a crystallographic operator such as a twofold axis.
> > The fourier transform of the electron density of the crystal is the 
> > convolution of the fourier transform of the individual molecules with the 
> > crystal lattice, with the fourier transform of the individual molecules 
> > usually giving the stronger contribution. So to get a solution with a 
> > decent R-factor, one must include all orientations (A, B etc.) in the 
> > model, with the position of the molecules in the crystal lattice 
> > contributing less to the diffraction pattern. So one can put the 
> > orientations on top of each other in a small unit cell using twinning, or 
> > put them in a larger unit cell at different positions using 
> > crystallographic or non-crystallographic symmetry. That is what I meant be 
> > "twinning" (N)CS.
> >
> > Hope this makes my remark a little clearer.
> >
> > Best,
> > Herman
> >
> > PS: While other BB readers may have had the same question, I have posted 
> > the reply to the BB. I hope you don't mind.
> >
> >
> > -Ursprüngliche Nachricht-
> > Von: Guan, Lan [mailto:lan.g...@ttuhsc.edu]
> > Gesendet: Donnerstag, 10. Januar 2019 20:53
> > An: Schreuder, Herman /DE
> > Betreff: 

Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning

[IGBMC]

Le Vendredi 11 Janvier 2019 09:07 CET, herman.schreu...@sanofi.com a écrit:

Dear Herman,
As far as I understood the twinning problem, what you say is only true in some 
occasions, and not in others.
If the "macroscopic" domains are so small that they are smaller than the X-rays 
coherence length, then you may do what you say because the X-rays emitted by 
the different domains can interfere.
But, if the domains become large, the X-rays emitted by the different domains 
do not interfere anymore and you have to add the weighted intensities, not the 
amplitudes, of each domain.
I hope I understood well your comment and did not "interfere negatively" with 
the thread...
Best
Philippe Dumas

> Dear Lan,
>
> Thank you for your compliment. I do not use Xtriage, so I did not bother 
> looking at the log files.
>
> What I meant to say is that with twinning, the crystal has different 
> macroscopic domains where the molecules have different orientations, say one 
> domain with orientation A and one domain with orientation B. Since these 
> domains grow on top of each other, they are usually related by a twin 
> operator similar to a crystallographic operator such as a twofold axis.
> The fourier transform of the electron density of the crystal is the 
> convolution of the fourier transform of the individual molecules with the 
> crystal lattice, with the fourier transform of the individual molecules 
> usually giving the stronger contribution. So to get a solution with a decent 
> R-factor, one must include all orientations (A, B etc.) in the model, with 
> the position of the molecules in the crystal lattice contributing less to the 
> diffraction pattern. So one can put the orientations on top of each other in 
> a small unit cell using twinning, or put them in a larger unit cell at 
> different positions using crystallographic or non-crystallographic symmetry. 
> That is what I meant be "twinning" (N)CS.
>
> Hope this makes my remark a little clearer.
>
> Best,
> Herman
>
> PS: While other BB readers may have had the same question, I have posted the 
> reply to the BB. I hope you don't mind.
>
>
> -Ursprüngliche Nachricht-
> Von: Guan, Lan [mailto:lan.g...@ttuhsc.edu]
> Gesendet: Donnerstag, 10. Januar 2019 20:53
> An: Schreuder, Herman /DE
> Betreff: Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning
>
> Dear Herman,
> I have read your insightful comments on twining and tNCS for years now, which 
> is very useful and helpful!  Thanks,
>
> For Donghyuk’s case, do you think that he really has a twinning issue?  With 
> a lower symmetry, all possible twining operators is always reported in the 
> Xtriage and did not mean a real twin existed.  His L test shows a twin 
> fraction of 0.00 in his log file.  The intensity statistics does not really 
> indicate an actually twinning.  Base on the refinement, twin law is needed to 
> get refinement going.  It looks like a twin.  I am confused...
>
> > the molecules are related by "twinning" (N)CS?
>
>
> What does this mean “ twinning (N)CS"?  Would you please kindly explain it 
> further?
>
> Thanks,
>
>
> Lan
>
>
> 
> Lan Guan, MD PhD
> Associate Professor | Department of Cell Physiology and Molecular Biophysics
> Director | Center for Membrane Protein Research
>
> 3601 4th St. MS 6551 | Lubbock, TX 79430
> 5A148A (Office) | (1) 806 743-3102 (Phone) | lan.g...@ttuhsc.edu (E-Mail)
>
> http://www.ttuhsc.edu/medicine/cell-physiology-molecular-biophysics/faculty/guan/
> https://www.ttuhsc.edu/centers-institutes/membrane-protein-research/

> 
>
> > On Jan 10, 2019, at 11:10 AM, herman.schreu...@sanofi.com wrote:
> >
> > CAUTION: This email originated from outside of TTUHSC. Do not click links 
> > or open attachments unless you recognize the sender and know the content is 
> > safe.
> >
> >
> > Dear Donghyuk,
> >
> > Unfortunately, everything is possible when NCS, twinning etc. get into the 
> > game. I do not have answers, but some questions for you to think about:
> > - Do you really have 6 twinning operators, or only one operator and are the 
> > other operators generated by (non)crystallographic symmetry?
> > - Both your P6322 cell and your C2 cell have angles of 90 90 90. For P6322, 
> > the last angle should be 120 and for C2, only the second angle is 
> > constrained to be 90. Maybe you should check that not somewhere something 
> > went wrong with the cell angles.
> > - How weak are the reflections that got discarded by halving the a- and 
> > b-axes? Do they have significant intensity, or is it only noise?
> > - By shrinking the unit cell, you may have created artificial twinning when 
> > in the large unit cell the molecules are related by "twinning" (N)CS.
> > - Since you seem to have found a solution with the small unit cell, you 
> > could see if you could 

Re: [ccp4bb] Compound with flexible conformation but nM Kd

[IGBMC]

Le Vendredi 27 Avril 2018 14:51 CEST, vincent Chaptal <vincent.chap...@ibcp.fr> 
a écrit:

Just a little remark (I hope I'm not splitting hairs): it is not exact that the 
alkyl chain "creates a lot of entropy". Instead the mark of dissolution of 
hydrophobic compounds in aqueous solvent is a strong decrease of entropy due to 
water molecules becoming ordered around the alkyl chain. This is precisely due 
to this  unfavorable entropic term that hydrophobic compounds do not dissolve 
in water, not because of an unfavorable enthalpic term.
Philippe D


> Dear Wenhe,
>
> A thought came to mind after having read all the other threads, for

> which I generally agree.
> An alkyl chain on a molecule (charged? hydrophilic?, you mention a
> negatively charged binding site) will most likely not lead to micelle
> formation as the cmc of the object will be most likely higher than the
> amount you use in solution, especially at uM concentrations. But the 
> alkyl chain nevertheless creates a lot of entropy, it doesn't like being
> in the water. How long is the alky chain? if it is 8-9-10 or even 11 
> carbons, it is likely to be not hydrophobic enough to want to burry the
> side chains into a micelle, and be very exchangeable in solution, yet
> not happy to be there. Binding onto a surface would reduce entropy,

> resulting in a better kon?
> You could try ITC, you will have access to detlaH and deltaG of binding,
> and by comparing with your other molecules maybe something would come up?
>
> please correct me if I'm wrong.
>
> All the best
> Vincent
>
> On 27/04/2018 05:07, WENHE ZHONG wrote:
> > Hi Philippe,
> >
> > The affinity was measured by SPR where we immobilized the protein on
> > the chip. One thing I forgot to mention is that the association rate
> > (kon) shown in SPR experiment for this compound is faster (>10-fold
> > faster) compared to other analogues with similar koff. There is a

> > pi-pi interaction between the scaffold structure and the protein
> > (tyrosine ring). Is it possible that the hydrophobic substituent could
> > facilitate the formation of this pi-pi interaction but not necessary
> > to involve in the interaction? Thanks.
> >
> > Kind regards,
> > Wenhe
> >
> >> On Apr 27, 2018, at 1:50 AM, DUMAS Philippe (IGBMC)
> >> <p.du...@ibmc-cnrs.unistra.fr <mailto:p.du...@ibmc-cnrs.unistra.fr>>
> >> wrote:
> >>
> >>
> >> Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG
> >> <wenhezhong.xmu@gmail.com <mailto:wenhezhong.xmu@gmail.com>>
> >> a écrit:
> >>
> >> Just to be sure: how was the nM affinity evaluated ? By in vitro

> >> measurements, or by obtaining an IC50 by tests on cells ?
> >> Of course, if you are mentioning an IC50, you may have a measurement
> >> of the efficacy of drug entrance in the cells, not just of specific
> >> binding to your protein target.
> >> Philippe D.
> >>
> >>> Dear Community,
> >>>
> >>> A little bit out of topic here. We are applying the structure-based
> >>> approach to design compounds that can bind our protein target. We
> >>> have synthesized a series of analogues based on the same scaffold
> >>> with different substituents at one particular site. The most potent
> >>> analogue (nM Kd) has a long alkyl chain substituent. We thought this
> >>> hydrophobic substituent should have strong interactions with the 
> >>> target protein leading to nM range affinity. However, crystal
> >>> structures show very weak densities for this substituent and no

> >>> obvious interaction between the substituent and the target protein,
> >>> suggesting that this long alkyl chain substituent is flexible
> >>> without binding to the protein. This binding site is relatively

> >>> negative charged according to the electrostatic potential analysis.
> >>>
> >>> So it is a puzzle to me that how this dynamic and hydrophobic alkyl
> >>> chain substituent can lead the compound to achieve nM affinity
> >>> (>10-fold better than any other substituent) — in particular the
> >>> binding site is not hydrophobic and no interaction is found between
> >>> the substituent and the protein.
> >>>
> >>> Anything I have miss here that can increase the binding affinity 
> >>> without interacting with the target?
> >>>
> >>> Thanks.
> >>>
> >>> Kind regards,
> >>> Wenhe
> >>>
> >>>
> >>>
> >>
> >>
> >>
> >>
> >>
> >>
> >
>
> --
>
> Vincent Chaptal, PhD
>
> Institut de Biologie et Chimie des Protéines
>
> Drug Resistance and Membrane Proteins Laboratory
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://www.ibcp.fr
>
>

Re: [ccp4bb] Compound with flexible conformation but nM Kd

[IGBMC]

Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG  a 
écrit:

Just to be sure: how was the nM affinity evaluated ? By in vitro measurements, 
or by obtaining an IC50 by tests on cells ?
Of course, if you are mentioning an IC50, you may have a measurement of the 
efficacy of drug entrance in the cells, not just of specific binding to your 
protein target.
Philippe D.

> Dear Community,
>
> A little bit out of topic here. We are applying the structure-based approach 
> to design compounds that can bind our protein target. We have synthesized a 
> series of analogues based on the same scaffold with different substituents at 
> one particular site. The most potent analogue (nM Kd) has a long alkyl chain 
> substituent. We thought this hydrophobic substituent should have strong 
> interactions with the target protein leading to nM range affinity. However, 
> crystal structures show very weak densities for this substituent and no 
> obvious interaction between the substituent and the target protein, 
> suggesting that this long alkyl chain substituent is flexible without binding 
> to the protein. This binding site is relatively negative charged according to 
> the electrostatic potential analysis.
>
> So it is a puzzle to me that how this dynamic and hydrophobic alkyl chain 
> substituent can lead the compound to achieve nM affinity (>10-fold better 
> than any other substituent) — in particular the binding site is not 
> hydrophobic and no interaction is found between the substituent and the 
> protein.
>
> Anything I have miss here that can increase the binding affinity without 
> interacting with the target?
>
> Thanks.
>
> Kind regards,
> Wenhe
>
>
>