Re: [ccp4bb] request for applications

[Nukri Sanishvili]

Hi James,
The elevator pitch has to be 90 degrees, no? Otherwise it would travel
horizontally as well.
Or, perhaps, we should petition these types of elevators to be added to
building codes for large, multi-entrance buildings?
Best,
Nukri

On Mon, Apr 1, 2024 at 10:08 AM James Holton  wrote:

> For you, Eleanor? Of course!  I look forward to it.
>
> But do you have an "elevator pitch"?
>
> I feel that a lively exchange of short messages conveys ideas much more
> efficiently and effectively than an annual exchange of hyper-dense
> documents.
>
> Cheers,
>
> -James Holton
> MAD Scientist
>
> On 4/1/2024 6:27 AM, Eleanor Dodson wrote:
>
> It. Will probably take me  a. Full year to draft the. Application - is
> that too slow?
>
> On Mon, 1 Apr 2024 at 09:22, Frank Von Delft <
> bcb385fe5582-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Oh dear, your prime number oversupply crashed the crypto Ponzi scheme
>> market.  Will you accept $10e2 proposals now?
>>
>> Sent from tiny silly touch screen
>> --
>> *From:* James Holton 
>> *Sent:* Monday, 1 April 2024 08:01
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] request for applications
>>
>> Hey Everyone,
>>
>> It may sound like an incredibly boring thing that there has never been a
>> formal mathematical proof that finding the prime factors of very large
>> numbers doesn't have a more efficient algorithm than simply trying every
>> single one of them. Nevertheless, to this day, encryption keys and
>> indeed blockchain-based cryptocurrencies hinge upon how computationally
>> hard it is to find these large prime factors. And yet, no one has ever
>> proven that there is not a more efficient way.
>>
>> It occurred to me recently that cryptocurrencies (blockchains) are
>> nothing more than a sequence of numbers, and Large Language Models
>> fundamentally take a sequence of "words" and predict the next one in the
>> series. So, they seem naturally suited to the task of finding a more
>> efficient way. I spent some of my free time trying my hand at this.
>> There were some twists and turns along the way, but as of today it seems
>> to be working. Predictions are now coming pretty fast. By the end of
>> April 1, I expect to have ~ $1e12 USD on current ledgers. This may have
>> certain socioeconomic ramifications, but that is not what I want to
>> discuss here. What I want to discuss is how to use this new source of
>> scientific funding!
>>
>> My question for the BB is: what would YOU do if you had $1e12 USD for
>> your science? No non-scientific proposals please. There are plenty of
>> other forums for those.  This BB is about biological structural science,
>> so please stay on-topic.  OK?  And now: suggestions!
>>
>> I am particularly interested in projects that can only be done with a
>> large, cooperative $1e12 USD, but not by 10e6 independent and unrelated
>> $100e3 projects. The Apollo moon missions, for example cost $300e9
>> (adjusted USD).  On a smaller scale, re-doing the whole PDB from cloning
>> and expression to crystallization and structure solution would only cost
>> about $500e6 USD. That would finally give us a good database of
>> crystallization conditions for training an AI to tell you, given a
>> sequence, what the crystallization conditions (if any) will be. That
>> might take a lot of computing power, but there is plenty left over to
>> buy 10 zettaflops of computing power (and the solar panels needed to
>> power it). Or, if we really want to just divide it up, that would be
>> $10e6 for each of the ~1e5 people on this planet who fit into the
>> category of "biological scientist". That's not just PIs, but postdocs,
>> grad students, techs. Everybody.
>>
>> I'm sure this will solve a lot of problems, but not all of them. And, I
>> like to get ahead of things. So, what are the non-financial problems
>> that will remain?  I think these are the most important problems in
>> science: the intellectual and technological hurdles that money can't
>> overcome.  I'm hoping this will be an opportunity for all of us to focus
>> on those.  I know we're all not used to thinking on this scale, but, at
>> least for today, let's give it a try!
>>
>> Looking forward to your applications,
>>
>> -James Holton
>> MAD Scientist
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>> --
>> *From:* James Holton 
>> *Sent:* Monday, 1 April 2024 08:01
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] request for applications
>>
>> Hey Everyone,
>>
>> It may sound like an incredibly boring thing that there has never been a
>> formal mathematical proof 

Re: [ccp4bb] Room temperature change from 25ºC to 20ºC

[Nukri Sanishvili]

Excellent idea, Mark!
I think the solution to your dilemma is rather straightforward: we
introduce a Winter Standard Room Temperature (WSRT) and a Summer Standard
Room Temperature (SSRT). This way, the folks from locales closer to the
equator can always use SSRT, while those from more temperate climates can
take advantage of using both WSRT and SSRT.
The added benefit of this approach will be inclusion of researchers closer
to either of the poles (which, forgive me for saying it, you so egregiously
omitted from your considerations). Similar to the tropics, they could use
just one standard - WSRT.
Hope it helps your and so many young scientists' careers.
Best wishes,
Nukri



On Mon, Apr 1, 2024 at 9:29 AM Mark  wrote:

> Room temperature change from 25ºC to 20ºC
>
> As a member of the inter-society standards commission St-Incent I have
> been asked to take the bearings of the structural biology community
> regarding a proposal to lower the universally understood room temperature
> from 25ºC (77º Fahrenheit) to 20ºC (68º Fahrenheit). Obvious advantages
> would be less heating necessary for experiments at this standard
> temperature. Given that laboratories nowadays are not commonly heated to
> this high temperature anyway, it does appear to make sense.
>
> Members of tropical and subtropical countries have already expressed
> opposition to the proposal, because they have to reach room temperature by
> cooling rather than heating, so for them the proposal would mean more CO2
> emissions, not less.
>
> Please express opinions to this list today, so that I have time to collate
> them before the local deadline of 28 December.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] An exciting school on MX in Bangkok, Thailand

[Nukri Sanishvili]

The workshop website at  https://seacoast.kmutt.ac.th/2024/

On Mon, Dec 4, 2023 at 8:21 PM Nukri Sanishvili  wrote:

> Dear potential applicants,
>
> This is a friendly reminder that the deadline for application to the
> crystallographic workshop in Bangkok, Thailand, is fast approaching.
> You don't want to miss this great opportunity to learn the fundamentals
> macromolecular of crystallography and CryoEM from some of the world's top
> experts, and work on your own projects with their guidance. In addition, if
> you have suitable crystals, you could collect data at the Diamond Light
> Source with the help of experts.
> The workshop is from* Jan. 29 to Feb 7, 2024 *and the application
> deadline is *Dec. 15.*
> For
> *the application form, the program, and all other details, please visit
> the workshop website:*
>
> On Sun, Oct 15, 2023 at 10:29 PM Nukri Sanishvili 
> wrote:
>
>> Dear All,
>>
>> We are very excited to let everyone know that after a Covid19-induced
>> pause, we are renewing our macromolecular crystallographic school 
>> “*South-East
>> Asian Crystallographic Overview And Systematic Training”* *(SEA COAST)**,
>> organized jointly by King Mongkut’s University of Technology, Thonburi
>> (KMUTT), and CCP4, as well as Garib Murshudov of MRC-LMB, UK and Ruslan
>> Sanishvili (Nukri), USA. *
>>
>> The next school will take place from January 29 to February 7 at KMUTT in
>> Bangkok, Thailand http://seacoast.kmutt.ac.th/
>>
>> Online applications are now accepted till* December 15, 2023 *
>> https://seacoast.kmutt.ac.th/2024/application/ and The selection results
>> will be announced on* December 22, 2023.*
>>
>> *SEA COAST *2024 will cover the fundamental concepts of macromolecular
>> X-ray crystallography and all aspects of protein structure solution process
>> from crystallization to structure refinement and deposition to PDB, as well
>> as lectures on Cryo EM and Neutron Crystallography. It will feature most of
>> the modern crystallographic software programs presented by software
>> developers.
>>
>> A big part of the school will be dedicated to hands-on sessions where the
>> participants will work on their own data and structures with the guidance
>> of world’s renowned experts.
>>
>> *A new addition *to the SEA COAST 2024 is the opportunity to collect
>> crystallographic data at Diamond Light Source (UK).
>>
>> For the program, the application form, and other details, please visit
>> the workshop website at http://seacoast.kmutt.ac.th/
>>
>> If you have any questions, please contact Dr. Leela Ruckthong of KMUTT at
>> leela@mail.kmutt.ac.th or Dr. Ruslan Sanishvili of Crystallographic
>> Education and Research Assistance (CERA) sannu...@gmail.com or
>> ruslan.s...@kmutt.ac.th
>>
>> On Behalf of the SEA COAST 2024 organizers,
>>
>> Ruslan sanishvili and Leela Ruckthong
>>
>



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Re: [ccp4bb] An exciting school on MX in Bangkok, Thailand

[Nukri Sanishvili]

Dear potential applicants,

This is a friendly reminder that the deadline for application to the
crystallographic workshop in Bangkok, Thailand, is fast approaching.
You don't want to miss this great opportunity to learn the fundamentals
macromolecular of crystallography and CryoEM from some of the world's top
experts, and work on your own projects with their guidance. In addition, if
you have suitable crystals, you could collect data at the Diamond Light
Source with the help of experts.
The workshop is from* Jan. 29 to Feb 7, 2024 *and the application deadline
is *Dec. 15.*
For
*the application form, the program, and all other details, please visit the
workshop website:*

On Sun, Oct 15, 2023 at 10:29 PM Nukri Sanishvili 
wrote:

> Dear All,
>
> We are very excited to let everyone know that after a Covid19-induced
> pause, we are renewing our macromolecular crystallographic school “*South-East
> Asian Crystallographic Overview And Systematic Training”* *(SEA COAST)**,
> organized jointly by King Mongkut’s University of Technology, Thonburi
> (KMUTT), and CCP4, as well as Garib Murshudov of MRC-LMB, UK and Ruslan
> Sanishvili (Nukri), USA. *
>
> The next school will take place from January 29 to February 7 at KMUTT in
> Bangkok, Thailand http://seacoast.kmutt.ac.th/
>
> Online applications are now accepted till* December 15, 2023 *
> https://seacoast.kmutt.ac.th/2024/application/ and The selection results
> will be announced on* December 22, 2023.*
>
> *SEA COAST *2024 will cover the fundamental concepts of macromolecular
> X-ray crystallography and all aspects of protein structure solution process
> from crystallization to structure refinement and deposition to PDB, as well
> as lectures on Cryo EM and Neutron Crystallography. It will feature most of
> the modern crystallographic software programs presented by software
> developers.
>
> A big part of the school will be dedicated to hands-on sessions where the
> participants will work on their own data and structures with the guidance
> of world’s renowned experts.
>
> *A new addition *to the SEA COAST 2024 is the opportunity to collect
> crystallographic data at Diamond Light Source (UK).
>
> For the program, the application form, and other details, please visit the
> workshop website at http://seacoast.kmutt.ac.th/
>
> If you have any questions, please contact Dr. Leela Ruckthong of KMUTT at
> leela@mail.kmutt.ac.th or Dr. Ruslan Sanishvili of Crystallographic
> Education and Research Assistance (CERA) sannu...@gmail.com or
> ruslan.s...@kmutt.ac.th
>
> On Behalf of the SEA COAST 2024 organizers,
>
> Ruslan sanishvili and Leela Ruckthong
>



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[ccp4bb] An exciting school on MX in Bangkok, Thailand

[Nukri Sanishvili]

Dear All,

We are very excited to let everyone know that after a Covid19-induced
pause, we are renewing our macromolecular crystallographic school “*South-East
Asian Crystallographic Overview And Systematic Training”* *(SEA COAST)**,
organized jointly by King Mongkut’s University of Technology, Thonburi
(KMUTT), and CCP4, as well as Garib Murshudov of MRC-LMB, UK and Ruslan
Sanishvili (Nukri), USA. *

The next school will take place from January 29 to February 7 at KMUTT in
Bangkok, Thailand http://seacoast.kmutt.ac.th/

Online applications are now accepted till* December 15, 2023 *
https://seacoast.kmutt.ac.th/2024/application/ and The selection results
will be announced on* December 22, 2023.*

*SEA COAST *2024 will cover the fundamental concepts of macromolecular
X-ray crystallography and all aspects of protein structure solution process
from crystallization to structure refinement and deposition to PDB, as well
as lectures on Cryo EM and Neutron Crystallography. It will feature most of
the modern crystallographic software programs presented by software
developers.

A big part of the school will be dedicated to hands-on sessions where the
participants will work on their own data and structures with the guidance
of world’s renowned experts.

*A new addition *to the SEA COAST 2024 is the opportunity to collect
crystallographic data at Diamond Light Source (UK).

For the program, the application form, and other details, please visit the
workshop website at http://seacoast.kmutt.ac.th/

If you have any questions, please contact Dr. Leela Ruckthong of KMUTT at
leela@mail.kmutt.ac.th or Dr. Ruslan Sanishvili of Crystallographic
Education and Research Assistance (CERA) sannu...@gmail.com or
ruslan.s...@kmutt.ac.th

On Behalf of the SEA COAST 2024 organizers,

Ruslan sanishvili and Leela Ruckthong



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Re: [ccp4bb] British X-ray Crystallographers

[Nukri Sanishvili]

Hi Elspeth,
You are right on the political correctness topic. However, the modern term
would be Garthem, not Garperson...
:)
Best,
Nukri

On Wed, May 24, 2023 at 5:14 AM Elspeth Garman <
elspeth.gar...@bioch.ox.ac.uk> wrote:

> Thanks a lot Harry! Unfortunately there is only one of me so it should
> indeed be ‘man’ not ‘men’, although in these days of political correctness
> it should really be ‘Garperson’!
> Also Microsoft often changes it to ‘ Garmin’.
> Best wishes
> Elspeth
>
> Sent from my iPhone
>
> > On 24 May 2023, at 10:56, Randy John Read  wrote:
> >
> > So have I! They’ll learn not to disrespect one of our favourite people.
> >
> > Randy
> >
> >> On 24 May 2023, at 10:44, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>
> >> Hi Gerard
> >>
> >> I’ve mentioned it to the organiser - we shall see how long the Garmen
> will be there!
> >>
> >> Harry
> >>
>  On 24 May 2023, at 10:27, Gerard Bricogne 
> wrote:
> >>>
> >>> Dear Jon,
> >>>
> >>>   Quite a line-up indeed.
> >>>
> >>>   Might someone at the RSC correct the typo in Elspeth's surname (in
> two
> >>> places)? Or is it a plural form ;-) ?
> >>>
> >>>
> >>>   With best wishes,
> >>>
> >>>Gerard
> >>>
> >>> --
> >>> On Tue, May 23, 2023 at 10:16:54PM +, Jon Cooper wrote:
>  I am biased, but this looks like an interesting meeting:
> 
> 
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
> 
>  Best wishes, Jon Cooper.
>  jon.b.coo...@protonmail.com
> 
>  Sent with [Proton Mail](https://proton.me/) secure email.
> 
> 
> 
> 
>  To unsubscribe from the CCP4BB list, click the following link:
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> 
>  This message was issued to members of
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> >>>
> >>>
> 
> >>>
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>>
> >>> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB,
> a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions
> are available at https://www.jiscmail.ac.uk/policyandsecurity/
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
> >> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB,
> a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions
> are available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> > -
> > Randy J. Read
> > Department of Haematology, University of Cambridge
> > Cambridge Institute for Medical Research Tel: +44 1223 336500
> > The Keith Peters Building
> > Hills Road   E-mail:
> rj...@cam.ac.uk
> > Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
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Re: [ccp4bb] Alexey Vagin

[Nukri Sanishvili]

Sad news indeed for so many of us, those who knew Alexei personally and
those who benefited professionally from his selfless dedication to
computational crystallography.
A wise man once said something along the lines of anyone successful today
standing on the shoulders of giants of the past. Unfortunately, Alexei has
just become one such giant.
I am so blessed to have known him professionally from my time at IKAN and
to have him as a friend. And I am sure this sentiment is shared by all his
colleagues and anyone who knew him personally.
Writing this with a very heavy heart, on behalf of my wife as well.
Nukri



On Sun, Mar 26, 2023 at 1:29 PM Eugene Krissinel - STFC UKRI <
6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from
> a heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular
> crystallography, to which he devoted his whole life. He is known for his
> BLANC Suite for structure solution done at the Moscow Institute of
> Crystallography in the 1980s, as well as for his contributions to Refmac
> and Monomer Library. Many thousands of researchers have benefited from his
> work on Molrep and Balbes software for Molecular Replacement. After his
> retirement in 2010, Alexey developed and actively maintained the MorDA
> software for MR, which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through
> his contributions to CCP4, where we will take the best care of his
> distinguished legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is
> very sad news,
>
> Eugene
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] Future Diffraction Methods

[Nukri Sanishvili]

Hi Pavel,
Your description of the current status is exactly correct. And that's
exactly what I am proposing to change or, more accurately, try to change.
By seeking out and  bringing together people who do complementary and
collaborative work, so they can set an example for others.
This, of course, isn't meant in place of more narrowly defined topical
meetings and conferences but to be in addition to those.
James asked the community if we had new ideas and this is a new-ish
approach I was suggesting.
Don't get me wrong - I myself will happily continue my efforts in more
narrowly defined meetings.
Best wishes,
Nukri

On Sun, Jan 29, 2023 at 6:44 PM Pavel Afonine  wrote:

> Nukri,
>
> IMO, the idea of cross-discipline meetings is great conceptually, at least
> for reasons you pointed out, but utopical in practice. When we attend our
> field-specific meetings we meet colleagues we know, we talk to
> collaborators from the past or find new ones, we have things in common that
> we can talk about to forge something new, we meet authors of papers we were
> excited to read, and so on, and so on.
> I once attended a meeting of some chemistry society, well, which is not
> too far from what we are doing, really, as interpreting atomic models is
> essentially putting your chemistry knowledge into production. And, at that
> meeting I felt like I'm alone in a dark forest.
> Now, I imagine, if you bring two (or more) groups of people to your
> meeting from two different domains, well, I guess you will end up having
> two bubbles of people clustered by their field of interest.
>
> Same disclaimer goes here as yours -- no offence to any one, just thinking
> out loud...
>
> All the best!
> Pavel
>
> On Sun, Jan 29, 2023 at 6:09 AM Nukri Sanishvili 
> wrote:
>
>> Hi James,
>> This meeting has indeed been one of the best ones by its format, content,
>> and atmosphere. Many thanks to all the organizers and attendees of the
>> past. Nevertheless, it is not surprising that it was cancelled, given the
>> trends in structural biology research. Straightforward evolutionary
>> pressure to adapt or else...
>>
>> Throughout my career I was always amazed (dare I say, annoyed?) how
>> scientists from different fields, or even the same field but different
>> methods, speak different languages. How little they understand each other,
>> become entrenched in their own methods and how much of the
>> collaboration/cooperation opportunities are wasted.
>>
>> IMO, having a conference on "Complementary Methods in Structural Biology"
>> with the emphasis on complementarity and not on individual methods, would
>> be a great benefit in the long run. Hopefully it would give good examples
>> to young researchers to help them develop a collaborative mindset.
>>
>> If I offended anyone, it was not intentional, I promise, and apologize in
>> advance.
>> Best wishes to all and best of luck to all who continue the effort for
>> the benefit of the whole community.
>> Nukri
>>
>>
>>
>>
>>
>> On Fri, Dec 16, 2022 at 4:11 PM James Holton  wrote:
>>
>>> I want to thank everyone who attended the 2022 Gordon Research
>>> Conference and Gordon Research Seminar on Diffraction Methods in
>>> Structural Biology, as well as all those who contributed to these great
>>> gatherings in the past.  It was an outstanding meeting if I do say so
>>> myself. Not just because it had been so long without in-person
>>> interaction, not just because we had zero covid cases (which I see as no
>>> small feat of Mind over Virus), but because of this amazing community.
>>> It is rare in this world to have such a strong spirit of collaboration,
>>> camaraderie and openness in undertakings as high-impact as this.
>>> Surmounting the barriers to atomic-detail imaging of biological systems
>>> has never been more exciting and more relevant.  I am proud to be a part
>>> of it, and honored to have served as Chair.
>>>
>>> It is therefore with heavy heart that I report to this community that I
>>> was the last Chair of the Diffraction Methods GRC.
>>>
>>> The GRC Conference Evaluation Committee
>>> (https://www.grc.org/about/conference-evaluation-committee/) voted this
>>> year to discontinue the Diffraction Methods GRC and GRS. This ends a
>>> 46-year tradition that I feel played a vital, and vibrant role in the
>>> work of the people who answer questions on this BB.  The reason given
>>> was insufficient attendance.  All other metrics, such as evaluation
>>> surveys and demographics were very strong. I have tri

Re: [ccp4bb] Future Diffraction Methods

[Nukri Sanishvili]

Hi James,
This meeting has indeed been one of the best ones by its format, content,
and atmosphere. Many thanks to all the organizers and attendees of the
past. Nevertheless, it is not surprising that it was cancelled, given the
trends in structural biology research. Straightforward evolutionary
pressure to adapt or else...

Throughout my career I was always amazed (dare I say, annoyed?) how
scientists from different fields, or even the same field but different
methods, speak different languages. How little they understand each other,
become entrenched in their own methods and how much of the
collaboration/cooperation opportunities are wasted.

IMO, having a conference on "Complementary Methods in Structural Biology"
with the emphasis on complementarity and not on individual methods, would
be a great benefit in the long run. Hopefully it would give good examples
to young researchers to help them develop a collaborative mindset.

If I offended anyone, it was not intentional, I promise, and apologize in
advance.
Best wishes to all and best of luck to all who continue the effort for the
benefit of the whole community.
Nukri





On Fri, Dec 16, 2022 at 4:11 PM James Holton  wrote:

> I want to thank everyone who attended the 2022 Gordon Research
> Conference and Gordon Research Seminar on Diffraction Methods in
> Structural Biology, as well as all those who contributed to these great
> gatherings in the past.  It was an outstanding meeting if I do say so
> myself. Not just because it had been so long without in-person
> interaction, not just because we had zero covid cases (which I see as no
> small feat of Mind over Virus), but because of this amazing community.
> It is rare in this world to have such a strong spirit of collaboration,
> camaraderie and openness in undertakings as high-impact as this.
> Surmounting the barriers to atomic-detail imaging of biological systems
> has never been more exciting and more relevant.  I am proud to be a part
> of it, and honored to have served as Chair.
>
> It is therefore with heavy heart that I report to this community that I
> was the last Chair of the Diffraction Methods GRC.
>
> The GRC Conference Evaluation Committee
> (https://www.grc.org/about/conference-evaluation-committee/) voted this
> year to discontinue the Diffraction Methods GRC and GRS. This ends a
> 46-year tradition that I feel played a vital, and vibrant role in the
> work of the people who answer questions on this BB.  The reason given
> was insufficient attendance.  All other metrics, such as evaluation
> surveys and demographics were very strong. I have tried to appeal, but
> I'm told the vote was unanimous and final. I understand that like so
> many conference organizing bodies the GRC is having to make tough
> financial decisions. I must say I disagree with this one, but it was not
> my decision to make.
>
> Many of the past and elected Chairs have been gathering and discussing
> how to replace the Diffraction Methods GRC/GRS going forward. Many great
> ideas, advice and perspectives have been provided, but that is a select
> group. I feel it is now time to open up this discussion to the broader
> community of structural methods developers and practitioners. There are
> some important questions to ask:
>
> * How do we define this community?
>  Yes, many of us do cryoEM too, but is that one methods meeting?
> or two?
> * Does this community need a new diffraction methods meeting?
>  As in one meeting or zero?
> * Should we merge with an existing meeting?
>  It would make logistics easier, but a typical GRC has 22 hours
> of in-depth presentations over 5 days.  The GRS is 7 hours over 2 days.
> As Chair, I found that was not nearly enough.
> * Where do you think structural methods are going?
>  I think I know, but I may be biased.
> * Should the name change?
>  From 1976 to 2000, it was "Diffraction Methods in Molecular
> Biology". The word "diffraction", BTW, comes from the Latin for
> "shattering of rays", and originally used to describe the iridescence of
> bird feathers. That's spectroscopy!
> How about:
>   "Structural Methods for the Departing of Rays"
>
> I'm sure there are many more questions, and better suggestions.  I look
> forward to enlightening discussions!  GRCs have always been about
> discussion, and I hope to keep that tradition alive in this community.
>
> -James Holton
> MAD Scientist
>
> 
>
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Re: [ccp4bb] Off topic: Are all storage dewars equal?

[Nukri Sanishvili]

Hi Carmien,
It appears to me that the dewars in your first link are those made by
Taylor Wharton. You can do a search with that name and hopefully find less
expensive options. We've used them for many years and they are good.
Another one, you could try, is VME https://mvebio.com/aluminum-dewars/
We've used them as well and they are good too.

Just make sure to order a dewar with a wide neck/wide mouth so that your
puck holder fits in.
Also, for holding just 7 pucks, you could get away with smaller and less
expensive dewar. However, smaller ones will need adding of LNG more
frequently, so you will have to pick your poison.
Good luck!
Nukri

On Tue, Jul 5, 2022 at 4:13 AM Carmien Tolmie 
wrote:

> Hello everyone,
>
> We want to buy a storage dewar that can house seven unipucks. I have seen
> dewars on the website of the crystallography suppliers (such as the HC35
> https://www.moleculardimensions.com/products/high-capacity-cryogenic-refrigerators),
> which is significantly more expensive than the run-off-the-mill cryogenic
> storage dewars (such as the Biocane73
> https://www.thermofisher.com/order/catalog/product/CK509X5).
>
> Is there something that makes the dewars from the crystallography
> suppliers special? Or can you use any type of cryogenic storage dewar to
> store the pucs?
>
> Thank you very much for your input.
>
> Best wishes,
>
> Carmien
>
>
>
> --
>
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Re: [ccp4bb] X-ray crystallography defense questions

[Nukri Sanishvili]

Hi Jessica,
Your subject being membrane proteins, I might ask a question if your
conclusions and claims are commensurate with the data quality but as
Eleanor says, it really depends on what you are actually claiming and what
kind of data you have.
Cheers,
Nukri

On Tue, Jun 14, 2022 at 10:59 AM Jessica Besaw  wrote:

> Hello CCP4!
>
> I am preparing for my PhD defense on X-ray crystallography of membrane
> proteins.
>
> So my ask from you folks is: *What X-ray crystallography questions would
> you ask in a PhD defense? *
>
> All questions - easy, tough, tricky - are welcome.
>
> Thank you kindly,
>
> Jessica Besaw
>
>
>
>
> --
>
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Re: [ccp4bb] pictures in emails

[Nukri Sanishvili]

Hi Frank, CCP4bb-ers,
While the progress in the digital world in 2021 over the 90s is undeniable
(which, unfortunately cannot be said about the analog world), we should
keep in mind that some institutional accounts may filter out the
"suspiciously" large emails.
I would not be surprised if some of these accounts end up blacklisting
repeat offenders - CCP4bb in this case.
Best wishes,
Nukri

On Mon, Jul 19, 2021 at 8:12 AM Frank von Delft 
wrote:

> Ahem.  Ed, Tim - the 90s called, they want want their disk space and email
> clients back.
>
> As a co-perpertrator of vast volumes of detector data, and religious
> proponent of text *formatting* as inseparable part part the message, I
> disagree that in the year 2021, your suggestion still conforms to
> netiquette.
>
> In case anybody was left with the impression that Tim and Ed's view was
> universal.
>
> frank
>
>
>
>
>
>
>
> On 19/07/2021 10:26, Tim Gruene wrote:
>
> Hi Ed, dear ccp4bbs
>
> I fully support your email!
>
> Most email clients have a tick box to include a plain text version in
> addition of the html-version in their preferences.
>
> Reading plain text emails instead of the html-version (which is also an
> available option for most email clients) is a very effective barrier
> against spam. People should take this into account, considering the
> global rise of ransomware attacks, with serious consequences to some
> large institutions and companies.
>
> It has always been good netiquette to at least include a text-version
> of your email.
>
> Cheers,
> Tim
>
> On Sun, 18 Jul 2021 11:17:26 -0400 Edward Berry  
> 
> wrote:
>
>
> Two suggestions for people sending pictures of electron density to
> the BB:
>
> 1. Reduce the size of the pictures-
> The two pictures in yesterday's email appear nice and small in my
> email client, but still illustrate what is being described. However
> they are actually 4032x3024 and 2040x1458 pixels, making for rather
> large emails. All that extra resolution is wasted unless the user
> opens the image directly ("view image"), and in any case is
> completely unnecessary for the point being made. I think about
> 600x600 pixels is plenty for almost anything you want to show in
> electron density. This does not require manipulation in photoshop or
> such- just reduce the size of the graphics window and take a
> screenshot of that window.
>
> 2. send the picture as an attachment rather than inline. That way it
> won't be included in all the replies. Or if the people replying could
> find some way to exclude pictures or formt the reply as plain-text,
> that would help.
>
> (No, I'm not receiving these emails via 1200 baud modem- but I like
> to save the messages for future reference. If the trend continues
> toward high-resolution inline screenshots, that will take a
> significant amount of disk space. And yes, I know there is an
> archive.) eab
>
> 
>
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>
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>
>
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Re: [ccp4bb] Strange indexing problem

[Nukri Sanishvili]

Hi Rob,
There is no information provided to think what might be the problem with
indexing. How confident are you in the direct beam coordinates?
Are any of the cell lengths long-ish?
It may not be enough but at a minimum, two images 90 degrees apart might be
helpful.
Preferably, they would be taken in the orientation with the best-looking
diffraction and 90 degrees away from it.
Also, if you could indicate presumed and refined direct beam positions on
those images, it could be informative.
Cheers,
Nukri

On Mon, Jul 5, 2021 at 8:55 AM Robert S Phillips  wrote:

> I collected data last week on crystals of tyrosine phenol-lyase obtained
> under new conditions.  The data have higher resolution than previous
> crystals, to 1.5 A.  However, I can't get them to index in any space group
> but P1.  Usually, the space group is P21212.  The self-rotation function is
> attached.  The P1 data will give a molecular replacement solution, but it
> does not refine below 0.46.  The P1 asymmetric unit fits a dimer, but the
> assembly is a tetramer.  In the map, I can see the difference peaks from
> the other dimer of the tetramer.  What could be causing this problem?
>
> Rob
>
> Robert S. Phillips
> Professor of Chemistry and of Biochemistry and Molecular Biology
> University of Georgia
> Athens, GA 30602
> Phone: (706) 542-1996
> Fax: (706) 542-9454
> E-mail: rsphill...@chem.uga.edu
> Web:  http://tryptophan.net
> 
>
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>
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Re: [ccp4bb] Suggestions to improve resolution of protein crystals

[Nukri Sanishvili]

Dear Saurab,
It's a shame these crystals do not diffract well - they look so good!
I assume the diffraction you saw was recorded at cryo temperatures? If so,
it is possible that you may be damaging the crystals during cryo-pretection
and cryo-cooling. Before you go too deep into changing the crystallization
conditions, I would suggest taking a shot or two at ambient temperatures
and see if the diffraction is any better. If so, you may need to optimize
the cryo protocol and not the crystallization conditions.
Regards,
Nukri

On Sun, Mar 21, 2021 at 1:04 PM Saurabh Upadhyay 
wrote:

> Dear All,
>
> I am trying to crystalize a protein, which occurs in monomeric (60kDa) and
> tetrameric (240kDa) form. *The protein during crystallization was in
> MES buffer pH-6 *and the method of crystallization was "*Sitting drop*"
> in "*Proplex*" condition. Some of the conditions in which crystals were
> obtained are:
>
> *1) 0.1M HEPES pH-7; 10% (w/v) PEG 4000*
> *2) 0.1M Tris, pH-8; 8% (w/v) PEG 8000*
> *3) 0.1M Tris, pH-8; 25% (v/v) PEG 400*
>
> For reference, I have attached the images of the crystals observed below.
>
> *However, the diffraction pattern obtained and the resolution of crystals
> were very poor. Even some mosaicity has been observed.  *
>
> Kindly suggest some methods or modifications, to improve the resolution
> and  diffraction pattern of the crystals obtained.
>
> Thanking You,
> Sincerely,
> Saurabh Upadhyay,
> Ph.D. Scholar
> c/o Dr. Ashok kumar Patel,
> Kusuma School of Biological Sciences,
> Indian Institute of Technology, Hauz Khas,
> New Delhi-110016, India
>
>
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>
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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Nukri Sanishvili]

Sorry, in my previous email I was oblivious to the fact that there was Fe.
Iron is almost certainly oxidized. So, if you started collecting data with
reduced iron, but it got oxidized during data collection, you are probably
using the parametrization for the reduced rather than oxidized one in the
refinement. I wonder if it is so and if going to the reduced state would
make a difference.
Best,
N.

On Mon, Feb 22, 2021 at 12:23 PM Pavel Afonine  wrote:

> Hi,
>
> as others pointed out electron rich elements tend to amplify imperfections
> visible in Fo-Fc maps. Consider:
> - refining occupancy of Fe, the site may be partially occupied;
> - refining f' and f'' if data are anomalous;
> - surrounding histidines may 'see' this Fe as a nonbonded interaction and
> thus repulsion terms may kick in and push Fe from its position. Try
> defining weak coordination bonds between Fe and respective nitrogens;
> - refining anisotropic ADP of Fe only.
>
> Good luck!
> Pavel
>
> On Mon, Feb 22, 2021 at 7:27 AM Patrick Needham 
> wrote:
>
>>
>> --
>>
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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Nukri Sanishvili]

Is the oxidation state of the coordinated atom, or the identity of that
atom correct?
If there was a very slightly bigger atom, it would take care of the
positive residual density and would push out the His side chains a little
bit, which in turn could take care of the negative ones.
Or, the same effect could be achieved if the coordination distances end up
being slightly longer by identifying the "correct" atom or oxidation state.
Good luck!
Nukri

On Mon, Feb 22, 2021 at 12:22 PM Patrick Needham 
wrote:

>
> --
>
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Re: [ccp4bb] Tiny rocks on my CX100 shipping dewar

[Nukri Sanishvili]

Hi John,
I think I know what might have happened:
Many of the MX beamlines at the APS use some sort of filler in the
containers where the LN2 is dumped. If I remember correctly, one of the
beamlines is using fine gravel for this purpose. Also, it is required that
before shipping, the dewars are emptied - i.e. don't contain liquid. Now,
imagine somebody dumping the liquid into the grave-filled container without
removing the blue cap and without holding the dewar in the air - i.e. the
top of the dewar with the cap on is slightly buried into the gravel. Upon
straightening the dewar up, the blue cap would scoop up a little bit of the
gravel. Distribution of the pebbles on your picture is also noteworthy. It
suggests the side where the pebbles are was the side dipped into the gravel.
You might want to discuss this with your beamline host.
Best,
Nukri

On Fri, Dec 4, 2020 at 10:05 AM Tanner, John J. 
wrote:

> When we opened our CX100 shipping dewar returned from APS via FedEx this
> week, we observed what appears to be tiny rocks on the rim below the foam
> neck core:
>
> https://www.dropbox.com/s/ky09a1vbm9t0mrl/CX100withrocks.png?dl=0
>
> Has anyone seen this before? Is this perhaps the absorbent material from
> the inside of the dewar?
>
> Thanks,
>
> Jack
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Associate Chair of Biochemistry
> Department of Biochemistry
> University of Missouri
> 117 Schweitzer Hall
> 503 S College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Email: tanne...@missouri.edu 
> https://cafnrfaculty.missouri.edu/tannerlab/
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
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Re: [ccp4bb] Tiny rocks on my CX100 shipping dewar

[Nukri Sanishvili]

Hi John,
These look like real pebbles. If so, they would not word as an absorbent.
It looks more like a bad joke. Was the FedEx driver expecting some kind of
Thanksgiving gift from you? Wait till Christmas time then to see the real
surprises...
Best,
Nukri

On Fri, Dec 4, 2020 at 10:05 AM Tanner, John J. 
wrote:

> When we opened our CX100 shipping dewar returned from APS via FedEx this
> week, we observed what appears to be tiny rocks on the rim below the foam
> neck core:
>
> https://www.dropbox.com/s/ky09a1vbm9t0mrl/CX100withrocks.png?dl=0
>
> Has anyone seen this before? Is this perhaps the absorbent material from
> the inside of the dewar?
>
> Thanks,
>
> Jack
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Associate Chair of Biochemistry
> Department of Biochemistry
> University of Missouri
> 117 Schweitzer Hall
> 503 S College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Email: tanne...@missouri.edu 
> https://cafnrfaculty.missouri.edu/tannerlab/
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
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>
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Re: [ccp4bb] polarizer

[Nukri Sanishvili]

Hi All,

Adding some more details to what's been said already. Only because I've
seen too many times the polarizers being used incorrectly.
First, you need two polarization filters which are typically called
polarizer and analyzer. First one (the polarizer) lets through only the
light waves of a certain polarization. Then one needs to rotate the other
one (analyzer) until there is no more light getting through. At this point
the analyzer blocks the light that was let through by the polarizer This is
what Diane referred to as 90 degrees. Please note that the
polarizer-analyzer plates stay parallel to each other. After that, a
crystal is placed between them and is rotated. Unless it is a crystal with
cubic symmetry, at some angles it will light up in beautiful colors and at
some angles it will not. This is because the crystal changes the
polarization of the light passing through and "90 degree setup" of the
polarizer/analyzer pair is no longer valid for newly polarized light.
Please note that using plastic plates in this context is not quite
appropriate. The plastic polymer itself changes the polarization as well
and therefore it breaks the main principle of this method. With plastic
interference, it will be impossible to reach complete darkening of the
field of view. I can almost hear a lot of people saying that they've used
it with plastic plates without a problem. I believe it to be the case but
it still doesn't make it right.
Best,
Nukri

On Sun, Aug 16, 2020 at 9:15 AM Matthias Zeug  wrote:

> Hi all,
>
>
>
> The polarizer-microscope in our facility is not working properly, and I
> have to check my plates using a standard stereo-microscope. As a
> workaround, I thought about buying one at Amazon, placing it on top of the
> plates and rotating it to still test for birefringence.
>
>
>
> The product is linked below. Does anyone have some experience with this
> kind of "homemade" system? And also (this might be a stupid question), does
> the product even work? As far as I know, the polarizers in the microscopes
> are linear polarizers, whereas the product linked below is a circular
> polarizer. I would also be happy for product recommendations (optimally
> available at the German Amazon).
>
>
>
> Cheers
>
>
>
> Matthias
>
>
>
> https://www.amazon.de/dp/B00XNMXYBY/ref=cm_sw_r_cp_apa_i_5YsoFbFQXTBP9
>
>
>
> ___
>
> Buchmann Institute of Molecular Life Sciences
>
> Goethe University Frankfurt
>
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>
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Re: [ccp4bb] Molecular replacement problem

[Nukri Sanishvili]

Hi Robert,
In addition to the great suggestions you already have received, maybe you
should also consider SIMBAD or similar programs? The behavior you are
describing is typical of, albeit not exclusive to, having crystallized a
contaminant protein.
Good luck!
Nukri


On Thu, Jun 18, 2020, 08:01 Robert S Phillips  wrote:

> I've been pulling out my hair with this for a few months now.  I have data
> sets to 2.6 A for a new enzyme in the aminotransferase superfamily.
> Unfortunately, the closest structure is only 25% identity.  MR with PHASER
> using the monomer was a complete failure.  Since the minimum structure of
> enzymes in the family is a dimer (the active site is formed at the
> monomer-monomer interface), I used dimers for MR with PHASER.  Most of the
> results were marginal, but one looks good.  However, it will not refine.
> Everything I have done with this solution has failed, simulated annealing,
> morphing, etc., it will not refine; AUTOBUILD and BUCCANEER with it do not
> give any useable models, since they have poor statistics and low
> completeness.  The output from PHASER is below.
>
> ** SINGLE solution
>
> ** Solution written to PDB file:  DGL_phaser.1.pdb
> ** Solution written to MTZ file:  DGL_phaser.1.mtz
>Solution annotation (history):
>SOLU SET  RFZ=18.9 TFZ=23.0 PAK=0 LLG=193 TFZ==8.3 LLG=994 TFZ==20.1
> PAK=0 LLG=994 TFZ==20.1
>SOLU SPAC P 2 2 21
>SOLU 6DIM ENSE ense_1 EULER  360.00.00.0 FRAC -0.00 -0.00 -0.00
> BFAC -0.12 MULT 2 #TFZ==20.1
>SOLU ENSEMBLE ense_1 VRMS DELTA -3.5403 #RMSD  2.08 #VRMS  0.89
>
> With LLG = 994 and TFZ = 20.1, isn't this a real solution?
>
> Robert S. Phillips
> Professor of Chemistry and of Biochemistry and Molecular Biology
> University of Georgia
> Athens, GA 30602
> Phone: (706) 542-1996
> Fax: (706) 542-9454
> E-mail: rsphill...@chem.uga.edu
> Web:  http://tryptophan.net
> 
>
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Re: [ccp4bb] A question of density

[Nukri Sanishvili]

Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without placing
anything in the unclear blob of your interest so to obtain the best
possible phases and hopefully improve the blob density as well.
Then you should let the BB see what that density looks like. Looking at
only the list of possibilities has very little value without seeing the
density itself.
Best wishes,
Nukri

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw  wrote:

> Hello friends,
>
> I have a "blob" of density in an active site of my protein.
>
> I am struggling to determine if I should place a water in this spot, if I
> should model it as a disordered water, if the density may be a ligand that
> I have not considered, or if it should be left as unaccounted for density.
> I would like to publish this structure without compromising the science.
>
> I have attached several possibilities that I have considered below.
>
> Any suggestions would be appreciated.
>
> Cheers!
>
> Jessica Besaw
>
>
>
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>
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[ccp4bb] Reminder: Crystallographic school in Thailand

[Nukri Sanishvili]

Dear Colleagues,
This is a friendly reminder that we will be organizing a second
crystallographic school in Bangkok, Thailand, January 21-29, 2020.
The school will cover all aspects of macromolecular crystallography and *a
big part will be dedicated to the practical problem-solving sessions where
the participants will work on their own data with the expert guidance.*

Many popular software programs, such as *CCP4, Global Phasing software,
Phenix, SHELX, ARCIMBOLDO, ARP/wARP, Auto-Rickshaw, Coot, DIALS, MOSFLM,
PISA, Phaser, XDS etc.* will be presented.

The list of confirmed speakers include:
C. Ballard, T. Bergfors, N. Devenish, P. Emsley, A. Forster, K. Hirata, R.
Joosten, S. Kantamneni, E. Krissinel, A. Lebedev, A. Leslie, G. Murshudov,
S. Panjikar, R. Read, M. Ruengjit, R. Sanishvili, M. Sammito, T.
Terwilliger and C. Vonrhein.
The application deadline is November 30, 2019.
The school program, the on-line application form and all other details can
be found on the school website https://seacoast.kmutt.ac.th/

We hope to see you in Bangkok in January!
Leela, Garib, Ronan, Charles and Nukri



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Re: [ccp4bb] SeMet data

[Nukri Sanishvili]

Hi Lindsey,
As I mentioned to you in the separate email, 180 degrees for each half is
too little.

Here I'll try to explain some more about SAD vs. MAD:
What I have observed at our beamlines is that the majority of those who
collect MAD data, do it as as an afterthought of SAD. Priority in these
experiments is given to SAD and after it is done, some folks decide to
collect more data at a different wavelength "just in case". There are two
big mistakes in this approach, also explaining why SAD so often "works
better than MAD":
1. Unless one collects the second wavelength from a fresh part of the
crystal, or from a different crystal, there is too much radiation damage in
the second data set. Therefore, the differences in the intensities are
mostly caused by radiation damage and not by anomalous or dispersive
signal. This, of course, kills phasing. This is how SAD can be "better"
than MAD.
In a proper experiment, both wavelengths must be given equal priority. I.e.
distribute the crystal life time equally between the two.
2. Another mistake also stems from the fact that the 2nd wavelength is
treated as "addition" to SAD. Whether it is optimal or not is a different
discussion but typically, the SAD data are collected at the absorption
peak. Then, for 2-wavelength, one collects inflection point. What is lost
in this approach is the whole purpose of a MAD experiment, which is to use
the dispersive signal along with the anomalous one. Dispersive signal
between the inflection point and the peak wavelengths is not so great. In a
good experiment, one of the wavelengths is at the inflection point (as a
must). One could argue that the other is not at the absorption peak but
above the peak (in energy) in order to increase the dispersive signal. How
much above, will depend on particular f' and f" plots. Further the better
for the dispersive signal, but you also want to retain good anomalous one.
So, some compromise needs to be made here.
Bottom line is that SAD and MAD are two different experiments and one is
not a simple expansion of the other. You need to make a decision which one
you are doing and collect data accordingly.

Cheers,
Nukri

On Tue, Aug 27, 2019 at 11:30 AM Doyle, Lindsey A 
wrote:

> Hi Nukri,
>
> Thanks so much for your response. I appreciate the advice.
> 1. Yes, I verified that the anomalous option is turned on during data
> processing. Always a good question to ask
> 2. I collected 180° for each half. I have not tried phasing just one half.
> I’ll give a try but with my space group being P 21 the completeness and
> redundancy might be pretty low. I have a couple inverse beam data sets with
> wedges of 5° but they were about the same as the ones with 1°
> 3. I’ve been collecting 0.5 sec exposures but without reducing the flux.
> This seems to be one of the most recommended things and will be definitely
> doing it on my next run.
> 4. I’ve tried both SAD and MAD with peak 12661 (0.9793 Å) and inflection
> 12658 (0.9795 Å)
>
> Thanks again,
> Lindsey
>
>
> On Aug 26, 2019, at 6:54 PM, Nukri Sanishvili  wrote:
>
> Hi Lindsey,
> Obviously, one would need a lot more information to properly diagnose the
> problem and I am sure much smarter people them me will ask you for that.
> But just to move the task by couple of steps, I want to point out couple of
> things.
> 1. Trivial question: did you have the anomalous option turned on during
> data processing? (Just like from the IT help - is your computer turned on?)
> 2. How much data did you collect for each half of the inverse beam
> geometry? If you have enough, try phasing with only one half. When done
> properly, inverse beam experiment is great but it can easily get tricky
> introducing systematic errors and thus swamping anomalous signal.  If you
> redo the inverse beam, use little wider wedges, say, 5-10 degrees.
> 3. I thought an example of diffraction image would not give any useful
> information but... Judging by how smooth the background is on your Pilatus
> image, I am guessing you have used a lot of exposure. Can you calculate how
> much dose did you put in your crystal? If you are going to re-do the
> experiment, I would suggest reducing the exposure level and collecting more
> data.
> 4. Because you are not showing f' and f" plots, I am guessing that you are
> doing SAD. If it fails and you end up redoing your experiment and you have
> crystals for it, you might want to try 2-wavelength MAD but for that you
> would need to know exactly where is inflection point and collect one of the
> datasets there.
>
> Good luck!
> Nukri
>
> On Mon, Aug 26, 2019 at 5:45 PM L. Doyle  wrote:
>
>> I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino
>> acids, incorporation verified by Mass Spec). I've already collected several
&

Re: [ccp4bb] SeMet data

[Nukri Sanishvili]

Hi Lindsey,
Obviously, one would need a lot more information to properly diagnose the
problem and I am sure much smarter people them me will ask you for that.
But just to move the task by couple of steps, I want to point out couple of
things.
1. Trivial question: did you have the anomalous option turned on during
data processing? (Just like from the IT help - is your computer turned on?)
2. How much data did you collect for each half of the inverse beam
geometry? If you have enough, try phasing with only one half. When done
properly, inverse beam experiment is great but it can easily get tricky
introducing systematic errors and thus swamping anomalous signal.  If you
redo the inverse beam, use little wider wedges, say, 5-10 degrees.
3. I thought an example of diffraction image would not give any useful
information but... Judging by how smooth the background is on your Pilatus
image, I am guessing you have used a lot of exposure. Can you calculate how
much dose did you put in your crystal? If you are going to re-do the
experiment, I would suggest reducing the exposure level and collecting more
data.
4. Because you are not showing f' and f" plots, I am guessing that you are
doing SAD. If it fails and you end up redoing your experiment and you have
crystals for it, you might want to try 2-wavelength MAD but for that you
would need to know exactly where is inflection point and collect one of the
datasets there.

Good luck!
Nukri

On Mon, Aug 26, 2019 at 5:45 PM L. Doyle  wrote:

> I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino
> acids, incorporation verified by Mass Spec). I've already collected several
> datasets (ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of
> anomalous signal during data processing. I'm most familiar with HKL2000,
> but I have tried XDS and DIALS auto-processing. Here is a scan:
> https://ibb.co/LZqm33p and here is an example of a frame:
> https://ibb.co/gR3ZR47. Each frame is 0.25° and I'm using inverse beam
> with wedge size 1°. Maybe I need to adjust my collection strategy? All
> previous datasets have been in space group P 21 with dimensions of approx.
> 24.5Å, 85Å, 40Å, 90°, 96.5°, 90°. I'm sure there are additional things I
> can be doing in HKL but I've run out of ideas. Any advice or
> recommendations would be appreciated. Please let me know if you need
> additional information.
>
> Thank you,
> Lindsey
>
> 
>
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Re: [ccp4bb] challenges in structural biology

[Nukri Sanishvili]

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
solved by NMR.
I think we've done quite well since then...
Best,
Nukri

On Mon, Jul 15, 2019 at 3:45 PM  wrote:

> Hi Tassos, Tim,
>
> I wonder why would you or anyone on this list worry whether biological
> questions that can be asked and answered with structures are relevant to
> justify the resources? I think there is abundant evidence that this is the
> case. Unless your point is that crystallography is now dead for all
> practical
> purposes... then yes, I fully agree :-) It would however be wrong to erase
> its
> historical contribution to understanding biology.
>
> Best wishes,
>
> Radu
>
>
> > 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 (crystal)
> >> structure sufficiently relevant to justify the resources?
> >>
> >> Best,
> >> Tim
> >>
> >>
> >>
> >> Am 15.07.2019 21:44, schrieb Holton, James M:
> >>> 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 as possible, these challenges will take the form
> of
> >>> friendly competitions with defined parameters, data, a scoring system,
> >>> and "winners", to be established along with other unpublished results
> >>> only at the meeting, as is tradition at GRCs.
> >>> But what are the principle challenges in biological structure
> >>> determination today?  I of course have my own ideas, but I feel like
> I'm
> >>> forgetting something.  Obvious choices are:
> >>> 1) getting crystals to diffract better
> >>> 2) building models into low-resolution maps (after failing at #1)
> >>> 3) telling if a ligand is really there or not
> >>> 4) the phase problem (dealing with weak signal, twinning and
> >>> pseudotranslation)
> >>> 5) what does "resolution" really mean?
> >>> 6) why are macromolecular R factors so much higher than small-molecule
> >>> ones?
> >>> 7) what is the best way to process serial crystallography data?
> >>> 8) how should one deal with non-isomorphism in multi-crystal methods?
> >>> 9) what is the "structure" of something that won't sit still?
> >>> What am I missing?  Is industry facing different problems than
> >>> academics?  Are there specific challenges facing electron-based
> >>> techniques?  If so, could the combined strength of all the world's
> >>> methods developers solve them?  I'm interested in hearing the voice of
> >>> this community.  On or off-list is fine.
> >>> -James Holton
> >>> MAD Scientist
> >>>
> 
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >>
> >> --
> >> --
> >> Tim Gruene
> >> Head of the Centre for X-ray Structure Analysis
> >> Faculty of Chemistry
> >> University of Vienna
> >>
> >> Phone: +43-1-4277-70202
> >>
> >> GPG Key ID = A46BEE1A
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
>
> --
> Radu Aricescu
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44-(0)1223-267049
> fax: +44-(0)1223-268305
> www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
>
> 
>
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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Nukri Sanishvili]

Hi Jakob,
If there is radiation damage, for every "new" positive density there should
be a negative density in the original position. From the pictures we've
seen, it seems unlikely.
Best,
Nukri

On Wed, Jul 10, 2019 at 10:21 AM Keller, Jacob 
wrote:

> How about radiation-damaged/smashed Sulphur? You could test this by
> refining occupancy of the cys S.
>
>
>
> JPK
>
>
>
> +
>
> 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 *Lumbini
> Yadav
> *Sent:* Wednesday, July 10, 2019 7:12 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Fo-Fc density close to cysteine residue
>
>
>
> Thank you for the valuable input
>
>
>
> On Wed, Jul 10, 2019 at 4:25 PM Eleanor Dodson 
> wrote:
>
> Well - that more or less proves the residue is a CYS - there is a peak in
> the PHAN map right on the S.
>
> And that the extra density does not contain an anomalous scatterer so is
> probably not a metal or a sulphate or...
>
>
>
> But that still doesnt explain WHAT it is . Sorry not to be more help..
>
>
>
> Eleanor
>
>
>
> On Wed, 10 Jul 2019 at 11:32, Lumbini Yadav  wrote:
>
> No I am using ccp4i. I tried doing SAD refinement in refmac and the output
> image is attached below .
>
> I do not seen density near cysteine that was visible in Fo-Fc map
>
>
>
> On Wed, Jul 10, 2019 at 3:40 PM Eleanor Dodson 
> wrote:
>
> The key word for refmac is ANOM MAPONLY
>
> Are you using GUI2?
>
> Eleanor
>
>
>
> On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav  wrote:
>
> I have soaked my crystals in  sodium dithionite a reducing agent. I have
> not done mass spec but sequence is confirmed
>
>
>
> On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel 
> wrote:
>
> Have you mass-speced the protein before crystallization to make sure it
> wasn’t derivatized during expression and/or purification, or compared the
> mass spec of the crystals verses purified protein? Any fancy reagents or
> other reductants used during purification?
>
> What about S-Acetyl-cysteine (3-letter code: SCY).
>
>
>
> Best,
>
>
>
> Dan
>
>
>
> Daniel A Bonsor PhD.
>
> Sundberg Lab
>
> Institute of Human Virology
>
> University of Maryland, Baltimore
>
> 725 W Lombard Street N370
>
> Baltimore
>
> Maryland
>
> MD 21201
>
> Tel: (410) 706-7457
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Lumbini
> Yadav
> *Sent:* Tuesday, July 09, 2019 5:22 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Fo-Fc density close to cysteine residue
>
>
>
> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the crystallization
> condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
> protein was in Tris and NaCl. Before freezing the crystals were soaked in
> mother liquor containing sodium dithionite.
>
>
>
> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
> all the screenings we do see some part of Fo-Fc density unaddressed at 3
> sigma.
>
>
>
> Does anyone have an idea about what this density could be? Covalent
> modification?
>
>
>
> Thanks.
>
>
>
>
>
> Kind regards,
>
> Lumbini
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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> 
>
>
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Re: [ccp4bb] how many crystallographers are there?

[Nukri Sanishvili]

Dear Scott,

For the grant application, better question might be how many structural
biologists are out there, because "a crystallographer" may be interpreted
differently depending who is reading the grant application: are these the
people who know crystallography, or people who solve structures using
crystallography? The former category doesn't necessarily fall under the
target audience for your grant application, but the latter does.
Furthermore, with "structural biologists" you can claim a larger impact
factor, IMO.
Best wishes,
Nukri

On Wed, May 29, 2019 at 1:54 PM Scott Horowitz  wrote:

> Hi all, I was recently asked how many biological
> crystallographers plus cryo-EM users there are in the world (in relation to
> how many people could therefore be theoretically impacted by Foldit
> electron density tools, for the purposes of grant funding). I'm a bit at a
> loss as to even what order of magnitude to provide. Any thoughts about how
> to estimate a number?
>
>
> Thanks,
>
> Scott
>
>
> Scott Horowitz, Ph.D.
>
> Assistant Professor
>
> Department of Chemistry & Biochemistry
>
> Knoebel Institute for Healthy Aging
>
> University of Denver
>
>
>
> ECS Building
>
> 2155 E. Wesley Ave
>
> Denver, CO 80208
>
> Phone: 303-871-4326
>
> Fax: 303-871-7915
>
> Email: scott.horow...@du.edu
>
> Office: Room 561   Lab: Room 505
>
>
> --
>
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Re: [ccp4bb] Unknown anomalous scatterer

[Nukri Sanishvili]

Hi Aleix,
Can you describe how you did the fluorescence scan, or share the plot
itself? I am asking this because you say you could discard Fe, Zn and As/Se
but you don't say anything about Cu which is in between these elements.
If you tried but could not discard Cu, then it could be your "Culprit".
Best,
Nukri

On Fri, Mar 15, 2019 at 4:17 PM Aleix Tarrés Solé 
wrote:

> Dear colleagues:
> Hereby, I would like to expose a problem I encountered during the data
> processing of one of my crystals. Recently I collected a full dataset of a
> native protein-DNA crystal at an energy of 12667KeV. To my surprise, after
> processing with XDS I can see that I have significant values of anomalous
> correlation up to 5 Angstrom resolution. Using the fluorescence scan on the
> beam, I could discard the presence of the following heavy atoms that could
> have ended up in my drop due to cross-contamination; Se, As, Fe, Zn and Pr.
> So far, my attempts to use this dataset for phasing have been sadly
> unsuccessful. I would like to know if somebody has experience in this kind
> of problem and can gently help with some advices.
>
> Thank you all in advance
>
> Aleix
>
>
> --
>
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Re: [ccp4bb] vitrification vs freezing

[Nukri Sanishvili]

s: An alternative way to avoid the argument and discussion all together 
is to use cryo-cooled.
Tim: You go to a restaurant, spend all that time and money and order a 
fruitcake?

Cheers,
N.

On 11/15/2012 11:59 AM, Tim Gruene wrote:

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Dear s,

I have heard this discussion before and reminds me of people claiming
strawberries were nuts - which botanically may be correct, but would
still not make me complain about strawberries in a fruit cake I
ordered at a restaurant.

My Pengiun English Dictionary states (amongst other explanations)
freeze: to make extremely cold, so as long as you think your article
is written in English, you did not say anything wrong, assuming your
readers are intelligent enough to understand what you are trying to
say - and in a crystallographic article, the process of 'freezing'
your crystal is most likely not your main point where you need to be
100% unambiguous.

Cheers,
Tim

On 11/15/2012 06:13 PM, Sebastiano Pasqualato wrote:

Hi folks, I have recently received a comment on a paper, in which
referee #1 (excellent referee, btw!) commented like this:

crystals were vitrified rather than frozen.

These were crystals grew in ca. 2.5 M sodium malonate, directly dip
in liquid nitrogen prior to data collection at 100 K. We stated in
the methods section that crystals were frozen in liquid nitrogen,
as I always did.

After a little googling it looks like I've always been wrong, and
what we are always doing is doing is actually vitrifying the
crystals. Should I always use this statement, from now on, or are
there english/physics subtleties that I'm not grasping?

Thanks a lot, ciao, s


- -- 
Dr Tim Gruene

Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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--
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov

Re: [ccp4bb] vitrification vs freezing

[Nukri Sanishvili]

Hi Ethan,

I am not a linguist of Greek or even of English but I would assume that 
the term cryo-cooling is advocated not by DRD but by the people who 
want to distinguish between cooling down to *cryogenic* temperatures and 
say, cooling from 25  C to 4 C.

Cheers,
N.

On 11/15/2012 12:45 PM, Ethan Merritt wrote:

On Thursday, November 15, 2012 10:14:54 am Raji Edayathumangalam wrote:

Hi Sebastiano,

Elspeth Garman howls bloody murder everytime someone says they froze
their crystals. I think her issue is with the description of the process of
successfully flashcooling crystals in the presence of cryoprotectants as
freezing. Freezing technically is understood to imply the formation of
hexagonal ice

Not according to common English usage or any of the dictionaries I
looked in.
E.g. American Heritage Dictionary:
   Freeze 1.a. To pass from the liquid to the solid state by loss of heat.

It needn't refer to water at all, although that is the most common context.
You can find instructions for freezing olive oil to preserve it;
when I lived in Madison one occassionally had to worry about frozen
engine oil;  a headline from earlier this year claimed
Russian rivers clogged with frozen oil.


while what one really means is the successful solidification
of water in a random orientation (vitrification) and the prevention of the
hexagonal ice.

Semantics semantics!

I'd stick with flashcooled or something along those lines.
Raji

Funny you should say that :-)
While I have never had a referred complain about frozen crystals,
I have had several complain that flash cooling is different from
immersing in liquid nitrogen.  I never figured out what they had
in mind, but have since tried to avoid the term flash cooling.

By the way, cryo-cooled must be a term advocated by
The Department of Redundancy Department.
cryo - From Greek kruos, icy cold

Ethan



--
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov