Since you want to think big, I would suggest as a challenge to solve
the 3-D atomic structure of a human chromosome. Not the proteins
encoded by the DNA, but the 3-D structure of an entire chromosome.
Only about 1 percent of DNA codes for proteins. To understand gene
regulation and what makes a
r spot where happen to be. And indeed,
>plants
>> have usually more genes then animals!
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>von
>> *John R Helliwell
>
ts
> have usually more genes then animals!
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *John R Helliwell
> *Gesendet:* Freitag, 20. September 2019 09:19
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXT
Donnerstag, 19. September 2019 08:51
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] challenges in structural biology
Dear James,
Well, 100,000 genes used to be the estimate of the size of the human genome.
(eg see
https://physicsworld.com/a/protein-crys
l and Motor Proteins)
> www.diark.org (diArk - a resource for eukaryotic genome research)
> www.webscipio.org (Scipio - eukaryotic gene identification)
>
> Von: CCP4 bulletin board Im Auftrag von John R
> Helliwell
> Gesendet: Donnerstag, 19. September 2019 08:51
> An: CCP4
Date: Thursday, September 19, 2019 at 1:51 AM
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: Re: [ccp4bb] challenges in structural biology
Dear James,
Well, 100,000 genes used to be the estimate of the size of the human genome.
(eg see
https://physicsworld.com/a/protein-crystallography-the-human
n: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] challenges in structural biology
Dear James,
Well, 100,000 genes used to be the estimate of the size of the human genome.
(eg see
https://physicsworld.com/a/protein-crystallography-the-human-genome-in-3-d/ )
It seems it has got easier, albeit still garg
Dear James,
Well, 100,000 genes used to be the estimate of the size of the human genome.
(eg see
https://physicsworld.com/a/protein-crystallography-the-human-genome-in-3-d/ )
It seems it has got easier, albeit still gargantuan, at ~30,000 genes to be
expressed into proteins.
Meanwhile funding
Thank you John, an excellent choice as always. Here is your trillion
dollars! Now, what are you going to do with it?
Do you think simply scaling up current technology could reach this
goal? More screens, more combinations, more compute cycles? Remember,
if you want the "genome/proteome"
Dear James,
Here you go, a “grand challenge” suggestion to consider for funding from the
“James Holton Foundation for structural biology research”:-
“The human genome/proteome in 3-D”
Greetings,
John
Emeritus Professor John R Helliwell DSc
> On 14 Sep 2019, at 02:39, James Holton wrote:
>
I would like to thank everyone who took the time to respond to my
question that started this thread. It is really good for me to get a
sense of the community perspective. Some debates were predictable,
others not. Many ideas I agree with, some not so much. All were
thought-provoking. I
Sorry to be late chiming in on this post (survived RAGBRAI). I think the
challenges (crystallization, perdeuteration) and benefits of neutron
crystallography (where are those protons) could be included. We are now in
an era of using cryotrapping with neutrons which I think is really cutting
edge
Hi
It's pretty much what the powder people do when using Rietveld refinement,
isn't it? As far as I know, they fit a calculated curve from their structure to
a 1D trace of the powder pattern (happy to be corrected on this). All you need
to do is extend this to 3D - there may be enough work
Dear James,
It would seem to me that an important issue is also: do get all information out
of our diffraction data? By integrating the Bragg peaks we usually neglect the
diffuse scattering that could potentially contain additional (dynamic)
structural information. This can be cloudy diffuse
On Behalf Of *Keller,
> Jacob
> *Sent:* Wednesday, 24 July 2019 4:18 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] challenges in structural biology
>
>
>
> What about developing a theory of how crystallization happens, i.e., what
> does the microscopic “pictur
Dear CCP4bb,
From my industrial perspective: The crystallisation bottleneck has probably
been fairly well addressed. High throughput screening using robotics and around
20ul of protein per screen is common. There are lots of screens to try even if
they are rather redundant in their content.
I take the view that I'm trying to communicate with as many people as
possible, without distracting them with my spelling . . . So go for US
spellings.
Sent from mobile
On Tue, 23 Jul 2019, 22:39 Goldman, Adrian,
wrote:
> ..and responding in the same vein:
>
> my OED says that its etymology
, which
Sarah mentioned, required half a million scored images, which took years to get
together.
Janet
From: CCP4 bulletin board On Behalf Of Keller, Jacob
Sent: Wednesday, 24 July 2019 4:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
What about
From: CCP4 bulletin board on behalf of Goldman, Adrian
Sent: Wednesday, July 24, 2019 7:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
..and responding in the same vein:
my OED says that its etymology also comes from the Latin sulfur, sulphura
..and responding in the same vein:
my OED says that its etymology also comes from the Latin sulfur, sulphura in
the plural. So there is an etymological basis for the ph, even if it doesn’t
come from Greek.
Plus, since when has etymological logic has _anything_ to do with English
spelling?
Hi
Going off at a tangent...
The accepted spelling by the Royal Society of Chemistry (i.e. the professional
body representing chemists in the U.K.) since at least the early 1990s has been
"sulfate" too. "Sulphur", etc, has been deprecated for quite some time. Why?
Well, there's no good
wn and will
> go beyond the GRC and the question asked by James.
>
>
> M
>
>
> From: CCP4 bulletin board on behalf of Kay Diederichs
>
> Sent: 23 July 2019 08:59:10
> To: ccp4bb
> Subject: Re: [ccp4bb] challenges in structural biology
>
> If
What about developing a theory of how crystallization happens, i.e., what does
the microscopic “picture” look like when crystals are forming, then predicting
based on that picture? I remember looking into these things about ten years
ago, and there were some cool things being done with various
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] challenges in structural biology
On a completely different tack, isn't the most pressing requirement in current
structural biology a really good method of characterizing macromolecular
samples before they are put onto cryoEM grids - ie
On a completely different tack, isn’t the most pressing requirement in
current structural biology a really good method of characterizing
macromolecular samples *before *they are put onto cryoEM grids – ie
analysing *and screening them *in solution.
For one thing I’m told those huge microscopes
Hi James – thx for starting a riveting thread.
(Of course) I agree with Dom, Janet, Artem and the cosmic cats that
crystallization is key.
I also agree with Artem a relatively modest investment in the fundamentals
of crystallization could make a big difference – even a 10% improvement in
On 7/23/19 3:35 AM, melanie.voll...@diamond.ac.uk wrote:
> No longer those 20 odd names for ammonium sulphate
You mean ammonium *sulfate*. As it is called across the pond. :)
On a related note on common nomenclature for recording crystallization
experiments that Janet brought up:
I find it odd
and will go
beyond the GRC and the question asked by James.
M
From: CCP4 bulletin board on behalf of Kay Diederichs
Sent: 23 July 2019 08:59:10
To: ccp4bb
Subject: Re: [ccp4bb] challenges in structural biology
If you look at the nice figure at the top
If you look at the nice figure at the top of the online article, do you believe
that this (or rather, the correct) arrangement of domains/ molecules can be
predicted from a couple of correlated mutations, and energy minimization? I
think AI is a long way from that. Finding the correct fold of
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
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
> 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
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
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Artem
Evdokimov
Sent: Monday, 22 July 2019 7:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
Dear Kay
I disagree that 'magic bullet' is impossible. I think the definition is wrong
here - magic bullet to me
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,
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
Hi All,
Agreed!
Crystallization methods have improved in some ways, but at least in my
experience the real energy barrier is usually knowing enough about the quirky
biochemistry of the particular idiosyncratic complex we happen to be working
on. That means that one may need a grant's
Hi Artem,
you are certainly correct in that James' points 2-9 would be moot if his point
1 were solved. But as long as this is not the case, we resort to work with few
and/or small and/or badly diffracting and/or non-isomorphous crystals, which
makes points 2-9 very relevant.
Maybe the
ax: (716) 898 8660
> Skype:eddie.snell Email: esn...@hwi.buffalo.edu
> Webpage: https://hwi.buffalo.edu/scientist-directory/snell/
>
> Heisenberg was probably here!
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.A
@JISCMAIL.AC.UK] On Behalf Of Holton,
James M
Sent: Monday, July 15, 2019 3:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] challenges in structural biology
Hello folks,
I have the distinct honor of chairing the next Gordon Research Conference on
Diffraction Methods in Structural Biology (July 26-31
t screening experiments
>> deposited.
>>
>>
>>
>>
>>
>>
>>
>> From: CCP4 bulletin board On Behalf Of Nukri
>> Sanishvili
>> Sent: 15 July 2019 23:09
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] challeng
y 2019 10:21:42
To: Susan Lea
Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk>
Subject: Re: [ccp4bb] challenges in structural biology
Hi Susan,
We are not naive if we care about using the limited resources of this planet
responsibly. This has nothing to do with whoever's favourite
Dear James,
It would seem to me that an important issue is also: do get all
information out of our diffraction data? By integrating the Bragg peaks
we usually neglect the diffuse scattering that could potentially contain
additional (dynamic) structural information. This can be cloudy diffuse
creening experiments
deposited.
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of Nukri
Sanishvili
Sent: 15 July 2019 23:09
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] challenges in structural biology
I know i
y 2019 10:21:42
To: Susan Lea
Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk>
Subject: Re: [ccp4bb] challenges in structural biology
Hi Susan,
We are not naive if we care about using the limited resources of this planet
responsibly. This has nothing to do with whoever's favourite
>>>> ask
>>>> or
>>>> answer biological questions... for these, whether we like it or not,
>>>> macromolecular crystallography (or NMR, even in cell) cannot be the
>>>> future.
>>>> In
>>>> my opinion :-)
>>>&
the crystallography is dead might be a bit premature, it is still
>>> king
>>> for depositions.
>>> In 2017 we had a large number of fragment screening experiments deposited.
>>> From: CCP4 bulletin board On Behalf Of Nukri
>>> Sanishvili
>>
@mrc-lmb.cam.ac.uk
Sent: 17 July 2019 10:21:42
To: Susan Lea
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] challenges in structural biology
Hi Susan,
We are not naive if we care about using the limited resources of this planet
responsibly. This has nothing to do with whoever's favourite method. I
>>>> answer biological questions... for these, whether we like it or not,
>>>> macromolecular crystallography (or NMR, even in cell) cannot be the
>>>> future.
>>>> In
>>>> my opinion :-)
>>>>
>>>> Best wishes,
>>
llography is dead might be a bit premature, it is still
>>>> king
>>>> for depositions.
>>>>
>>>>
>>>>
>>>> In 2017 we had a large number of fragment screening experiments deposited.
>>>>
>>>>
>&
>>
>>
>>> Stating the crystallography is dead might be a bit premature, it is still
>>> king
>>> for depositions.
>>>
>>>
>>>
>>> In 2017 we had a large number of fragment screening experiments deposited.
>>>
>>
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
I think we are naive if we care about the method used to obtain the structure -
what matters is getting at the structure. What is great is that the variety of
ways we can do this has increased meaning more samples become tractable
t;
>>
>> In 2017 we had a large number of fragment screening experiments deposited.
>>
>>
>>
>>
>>
>>
>>
>> From: CCP4 bulletin board On Behalf Of Nukri
>> Sanishvili
>> Sent: 15 July 2019 23:09
>> To: C
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
I know it is going to hijack the original topic but I could not
help...
“The reports of death of (macromolecular) crystallography are
greatly
exaggerated.
If we believed the prognosticators, it has been dead since the
On Tue, 16 Jul 2019 18:02:20 +
"selina.st...@diamond.ac.uk" wrote:
> following up on Kay's point, I think it might be worth to discuss
> what we as a community understand by serial crystallography and what
> makes it different from multiple crystal crystallography. I recently
> gave a talk
Dear All,
I have been enjoying “lurking” on this thread - some thoughts
I love this approach to conference organising :-)
You missed radiation damage from this list ;-) - is critically connected to
isomorphism, resolution, serial methods and is probably the single greatest
limitation on
eening experiments
deposited.
>
>
>
>
>
>
>
>
From: CCP4 bulletin board On Behalf Of
Nukri
> Sanishvili
> Sent: 15 July 2019 23:09
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] challenges in structural biology
>
>
>
> I
itions.
>
>
>
> In 2017 we had a large number of fragment screening experiments deposited.
>
>
>
>
>
>
>
> From: CCP4 bulletin board On Behalf Of Nukri
> Sanishvili
> Sent: 15 July 2019 23:09
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] chall
Subject: Re: [ccp4bb] challenges in structural biology
I know it is going to hijack the original topic but I could not help...
“The reports of death of (macromolecular) crystallography are greatly
exaggerated.
If we believed the prognosticators, it has been dead since the 80s when some
folks
Hi all,
following up on Kay's point, I think it might be worth to discuss what we as a
community understand by serial crystallography and what makes it
different from multiple crystal crystallography. I recently gave a talk about
multiple-crystal and serial crystallography at a course and I
Hello James,
I like your list, but I wonder how much of this can be covered in meaningful
depth during a single GRC.
Your item
>7) what is the best way to process serial crystallography data?
deserves differentiation; there is a huge gap between serial synchrotron
crystallography (SSX) with
Hi James,
what about the use of highly anisotropic data, what it means in terms of
macromolecule arrangement within the crystal, and how to use the data
appropriately? An obvious link to item 5) and what resolution is in such
case?
An opening to item 6) and contribution of solvent as
6:34:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
1.1 Getting many diverse conformations routinely into well-diffracting
crystals; and knowing how to interpret them biologically.
On 15/07/2019 20:44, Holton, James M wrote:
> Hello folks,
>
> I have
1.1 Getting many diverse conformations routinely into well-diffracting
crystals; and knowing how to interpret them biologically.
On 15/07/2019 20:44, Holton, James M wrote:
> Hello folks,
>
> I have the distinct honor of chairing the next Gordon Research
> Conference on Diffraction Methods in
Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
Dear James,
10) are the biological questions that you can answer with a (crystal) structure
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology
Dear James,
10) are the biological questions that you can answer with a (crystal
it was worth it to the folks that got their name on the paper...
Cheers, tom
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural
2019 5:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] challenges in structural biology
Hello folks,
I have the distinct honor of chairing the next Gordon Research
Conference on Diffraction Methods in Structural Biology (July 26-31
2020). This meeting will focus on the biggest challenges cur
Hi James,
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage ---
RT serial crystallography
Temperature vs multiple
conformers
Thanks,
Minmin
> Dear James,
>
> 10) are
Hi James,
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage ---
RT serial crystallography
Temperature vs multiple
conformers
Thanks,
Minmin
> Dear James,
>
> 10) are
Hi James,
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage ---
RT serial crystallography
Temperature vs multiple
conformers
Thanks,
Minmin
> Dear James,
>
> 10) are
Hi James,
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage ---
RT serial crystallography
Temperature vs multiple
conformers
Thanks,
Minmin
> Dear James,
>
> 10) are
Hi James,
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage ---
RT serial crystallography
Temperature vs multiple
conformers
Thanks,
Minmin
> Dear James,
>
> 10) are
I know it is going to hijack the original topic but I could not help...
“The reports of death of (macromolecular) crystallography are greatly
exaggerated.
If we believed the prognosticators, it has been dead since the 80s when
some folks made the claim that the only relevant structures were those
I would wonder more if the biological questions you can *ask* with a (crystal)
structure are sufficiently relevant to justify the resources.
Sent from my iPhone
> On 15 Jul 2019, at 22:08, Tim Grüne wrote:
>
> Dear James,
>
> 10) are the biological questions that you can answer with a
Hello folks,
I have the distinct honor of chairing the next Gordon Research
Conference on Diffraction Methods in Structural Biology (July 26-31
2020). This meeting will focus on the biggest challenges currently
faced by structural biologists, and I mean actual real-world
challenges. As much
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