Re: [ccp4bb] Future Diffraction Methods

[Harry Powell]

My (limited) experience of the Diffraction Methods GRC suggests that the most 
valuable part of these meetings is when people get together outside the talks - 
so independent of the session chairs (apart from the people that they invite) 
and of any instructions given to speakers.

Just my two ha’porth

Harry

> On 30 Jan 2023, at 11:54, Frank von Delft  wrote:
> 
> Whether cross-pollination happens depends on the session chairs, and the 
> remit they're given, and the instructions given to the speakers:  if early on 
> everybody sets the tone, to inform as much as advertise, then it could be a 
> rip-roaringly interesting meeting.
> 
> At least, I've never encountered a method that was beyond my or any of my 
> students' comprehension, at least at some high level, provided we were 
> allowed to ask questions about it.
> 
> Frank
> 
> 
> 
> On 30/01/2023 10:40, Gerard Kleywegt wrote:
>> Hi all,
>> 
>> I'm a big believer in cross-pollination between disciplines. I think there 
>> could be room for a multidisciplinary methods meeting (MMM) provided the 
>> right topics are chosen. If these are things that concern NMR-ists, 
>> X-ray-ans and cryo-EM-ers equally you might get the right mix of people in 
>> the room and exchange of ideas and experiences with it. For example, all 
>> three use Maximum Likelihood (ML) methods. All three are or possibly will be 
>> interested in applying Machine Learning (e, ML) methods (e.g., in 
>> cryo-EM these have already been used for automatic particle picking and map 
>> improvement). And they all need to worry about validating models based on 
>> predicted models.
>> 
>> Having said that, I think there is also a need for specialised, 
>> method-specific meetings, but the two types of meeting are not mutually 
>> exclusive.
>> 
>> My 2 öre,
>> 
>> --Gerard
>> 
>> 
>> 
>> On Mon, 30 Jan 2023, Alexandre Ourjoumtsev wrote:
>> 
>>> Hi, everybody, hi, Nukri and Pavel !
>>> 
>>> I fully agree with Pavel that, if the speakers are not exceptional, if they 
>>> are (as usually) concentrated on their specific and narrow problems, 
>>> cross-discipline meetings make us lost quite fast, they are annoying and 
>>> useless. Richard Feynmann had the same experience, according to his books 
>>> :-)
>>> 
>>> At such meetings, people need to have a common point. However, it may be a 
>>> point different from the SUBJECT of the research. This may be common TOOLS. 
>>> And this indeed may lead to new ideas and results, maybe great ones.
>>> 
>>> There is a many-years positive experience of such meetings in Pushchino in 
>>> 80ths (both of you know this place; for other readers of this post - this 
>>> was indeed a great place !). Closer to our community, as I remember, Paul 
>>> Adams and John Spence organized such kind of meetings about 20 years ago in 
>>> US. I guess I know practical results from both these groups of meetings. 
>>> Some Crystallographic Computing Schools also try to act a little bit 
>>> "around the tools".
>>> 
>>> Why do not we think specifically in THIS direction (which is actually what 
>>> Nukri said, right? and somehow not so far from the previous GRC?) ?
>>> This is hard but feasible. But indeed hard :-(
>>> 
>>> Best regards to everybody,
>>> and many thanks to James for raising the problem !
>>> 
>>> Sacha Urzhumtsev
>>> 
>>> - Le 30 Jan 23, à 2:38, Nukri Sanishvili  a écrit :
>>> 
 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 < [ 
 mailto:pafon...@gmail.com |
 pafon...@gmail.com ] > 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 

Re: [ccp4bb] Future Diffraction Methods

[Frank von Delft]

Whether cross-pollination happens depends on the session chairs, and the 
remit they're given, and the instructions given to the speakers:  if 
early on everybody sets the tone, to inform as much as advertise, then 
it could be a rip-roaringly interesting meeting.


At least, I've never encountered a method that was beyond my or any of 
my students' comprehension, at least at some high level, provided we 
were allowed to ask questions about it.


Frank



On 30/01/2023 10:40, Gerard Kleywegt wrote:

Hi all,

I'm a big believer in cross-pollination between disciplines. I think 
there could be room for a multidisciplinary methods meeting (MMM) 
provided the right topics are chosen. If these are things that concern 
NMR-ists, X-ray-ans and cryo-EM-ers equally you might get the right 
mix of people in the room and exchange of ideas and experiences with 
it. For example, all three use Maximum Likelihood (ML) methods. All 
three are or possibly will be interested in applying Machine Learning 
(e, ML) methods (e.g., in cryo-EM these have already been used for 
automatic particle picking and map improvement). And they all need to 
worry about validating models based on predicted models.


Having said that, I think there is also a need for specialised, 
method-specific meetings, but the two types of meeting are not 
mutually exclusive.


My 2 öre,

--Gerard



On Mon, 30 Jan 2023, Alexandre Ourjoumtsev wrote:


Hi, everybody, hi, Nukri and Pavel !

I fully agree with Pavel that, if the speakers are not exceptional, 
if they are (as usually) concentrated on their specific and narrow 
problems, cross-discipline meetings make us lost quite fast, they are 
annoying and useless. Richard Feynmann had the same experience, 
according to his books :-)


At such meetings, people need to have a common point. However, it may 
be a point different from the SUBJECT of the research. This may be 
common TOOLS. And this indeed may lead to new ideas and results, 
maybe great ones.


There is a many-years positive experience of such meetings in 
Pushchino in 80ths (both of you know this place; for other readers of 
this post - this was indeed a great place !). Closer to our 
community, as I remember, Paul Adams and John Spence organized such 
kind of meetings about 20 years ago in US. I guess I know practical 
results from both these groups of meetings. Some Crystallographic 
Computing Schools also try to act a little bit "around the tools".


Why do not we think specifically in THIS direction (which is actually 
what Nukri said, right? and somehow not so far from the previous GRC?) ?

This is hard but feasible. But indeed hard :-(

Best regards to everybody,
and many thanks to James for raising the problem !

Sacha Urzhumtsev

- Le 30 Jan 23, à 2:38, Nukri Sanishvili  a 
écrit :



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 < [ 
mailto:pafon...@gmail.com |

pafon...@gmail.com ] > 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 < [ 
mailto:sannu...@gmail.com |

sannu...@gmail.com ] > 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 

Re: [ccp4bb] Future Diffraction Methods

[Gerard Kleywegt]

Hi all,

I'm a big believer in cross-pollination between disciplines. I think there 
could be room for a multidisciplinary methods meeting (MMM) provided the right 
topics are chosen. If these are things that concern NMR-ists, X-ray-ans and 
cryo-EM-ers equally you might get the right mix of people in the room and 
exchange of ideas and experiences with it. For example, all three use Maximum 
Likelihood (ML) methods. All three are or possibly will be interested in 
applying Machine Learning (e, ML) methods (e.g., in cryo-EM these have 
already been used for automatic particle picking and map improvement). And 
they all need to worry about validating models based on predicted models.


Having said that, I think there is also a need for specialised, 
method-specific meetings, but the two types of meeting are not mutually 
exclusive.


My 2 öre,

--Gerard



On Mon, 30 Jan 2023, Alexandre Ourjoumtsev wrote:


Hi, everybody, hi, Nukri and Pavel !

I fully agree with Pavel that, if the speakers are not exceptional, if they are 
(as usually) concentrated on their specific and narrow problems, 
cross-discipline meetings make us lost quite fast, they are annoying and 
useless. Richard Feynmann had the same experience, according to his books :-)

At such meetings, people need to have a common point. However, it may be a 
point different from the SUBJECT of the research. This may be common TOOLS. And 
this indeed may lead to new ideas and results, maybe great ones.

There is a many-years positive experience of such meetings in Pushchino in 80ths (both of 
you know this place; for other readers of this post - this was indeed a great place !). 
Closer to our community, as I remember, Paul Adams and John Spence organized such kind of 
meetings about 20 years ago in US. I guess I know practical results from both these 
groups of meetings. Some Crystallographic Computing Schools also try to act a little bit 
"around the tools".

Why do not we think specifically in THIS direction (which is actually what 
Nukri said, right? and somehow not so far from the previous GRC?) ?
This is hard but feasible. But indeed hard :-(

Best regards to everybody,
and many thanks to James for raising the problem !

Sacha Urzhumtsev

- Le 30 Jan 23, à 2:38, Nukri Sanishvili  a écrit :


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 < [ mailto:pafon...@gmail.com |
pafon...@gmail.com ] > 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 < [ mailto:sannu...@gmail.com |
sannu...@gmail.com ] > 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 

Re: [ccp4bb] Future Diffraction Methods

[Alexandre Ourjoumtsev]

Hi, everybody, hi, Nukri and Pavel ! 

I fully agree with Pavel that, if the speakers are not exceptional, if they are 
(as usually) concentrated on their specific and narrow problems, 
cross-discipline meetings make us lost quite fast, they are annoying and 
useless. Richard Feynmann had the same experience, according to his books :-) 

At such meetings, people need to have a common point. However, it may be a 
point different from the SUBJECT of the research. This may be common TOOLS. And 
this indeed may lead to new ideas and results, maybe great ones. 

There is a many-years positive experience of such meetings in Pushchino in 
80ths (both of you know this place; for other readers of this post - this was 
indeed a great place !). Closer to our community, as I remember, Paul Adams and 
John Spence organized such kind of meetings about 20 years ago in US. I guess I 
know practical results from both these groups of meetings. Some 
Crystallographic Computing Schools also try to act a little bit "around the 
tools". 

Why do not we think specifically in THIS direction (which is actually what 
Nukri said, right? and somehow not so far from the previous GRC?) ? 
This is hard but feasible. But indeed hard :-( 

Best regards to everybody, 
and many thanks to James for raising the problem ! 

Sacha Urzhumtsev 

- Le 30 Jan 23, à 2:38, Nukri Sanishvili  a écrit : 

> 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 < [ mailto:pafon...@gmail.com |
> pafon...@gmail.com ] > 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 < [ 
>> mailto:sannu...@gmail.com |
>> sannu...@gmail.com ] > 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 < [ mailto:jmhol...@lbl.gov |
>>> jmhol...@lbl.gov ] > 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

Re: [ccp4bb] Future Diffraction Methods

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi All

One of the joys of this meeting to me is that it is *not* about the science 
results and instead explicitly about how you get to those results. I worry that 
any meeting focussed on complimentary methods would inevitably coalesce around 
the common themes - science results - and become yet another structural biology 
conference.

I appreciate the needs for structural biology conferences, but I would feel 
that they are already well met. The diffraction methods conference is unique in 
allowing methods people to get together - if we expand this to all biophysical 
/ biochemical methods then we completely lose that. Even if we did succeed in 
pulling in methods people from all techniques, the meeting would then become 
too big.

I am well aware that the majority of people in the community are interested in 
the results not the methods, and are hence interested in applying as many 
techniques as necessary to get the insights. I’d just like to make sure that 
there is a little corner left where the people who develop those techniques - 
which are usually pretty specialist - can get together. I am certain that folks 
in non-diffraction methods development feel the same.

All the best Graeme



On 30 Jan 2023, at 01:59, Bostjan Kobe 
mailto:b.k...@uq.edu.au>> wrote:

Hi guys

I would be a bit more optimistic about this idea… If people attend the meeting 
with the objective of building some bridges they will try.  I have been to 
meetings on a biological topic where I may have been the only structural 
biologist but it was clear why I was there and I did not feel isolated, despite 
not being able to participate in every technical discussion on methods I am not 
familiar with.

Bostjan

--
Bostjan Kobe FAA
Australian Laureate Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences
and Institute for Molecular Bioscience (Division of Chemistry and Structural 
Biology) and Australian Infectious Diseases Research Centre
Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: 
b.k...@uq.edu.au
URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do not 
make any use of its contents. I do not waive any privilege, confidentiality or 
copyright associated with it. Unless stated otherwise, this e-mail represents 
only the views of the Sender and not the views of The University of Queensland.



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Nukri Sanishvili mailto:sannu...@gmail.com>>
Reply to: Nukri Sanishvili mailto:sannu...@gmail.com>>
Date: Monday, 30 January 2023 at 11:40 am
To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Future Diffraction Methods

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 
mailto:pafon...@gmail.com>> 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 
mailto:sannu...@gmail.com>> 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 researc

Re: [ccp4bb] Future Diffraction Methods

[Bostjan Kobe]

Hi guys

I would be a bit more optimistic about this idea… If people attend the meeting 
with the objective of building some bridges they will try.  I have been to 
meetings on a biological topic where I may have been the only structural 
biologist but it was clear why I was there and I did not feel isolated, despite 
not being able to participate in every technical discussion on methods I am not 
familiar with.

Bostjan

--
Bostjan Kobe FAA
Australian Laureate Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences
and Institute for Molecular Bioscience (Division of Chemistry and Structural 
Biology) and Australian Infectious Diseases Research Centre
Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: 
b.k...@uq.edu.au
URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do not 
make any use of its contents. I do not waive any privilege, confidentiality or 
copyright associated with it. Unless stated otherwise, this e-mail represents 
only the views of the Sender and not the views of The University of Queensland.



From: CCP4 bulletin board  on behalf of Nukri Sanishvili 

Reply to: Nukri Sanishvili 
Date: Monday, 30 January 2023 at 11:40 am
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] Future Diffraction Methods

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 
mailto:pafon...@gmail.com>> 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 
mailto:sannu...@gmail.com>> 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 
mailto:jmhol...@lbl.gov>> 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 ra

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 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 

Re: [ccp4bb] Future Diffraction Methods

[Pavel Afonine]

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 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 

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
>
> 
>
> 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/
>



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Future Diffraction Methods

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear All,

This was not really discussed widely at the study weekend however I think we 
have a core group of people who are sufficiently committed to the “GRC on 
diffraction methods” cause that we will keep it alive - as chair elect I also 
hold a very strong belief that we should keep this going.

Currently we are exploring the opportunities for the “not the GRC on 
diffraction methods 2024” with an intent on keeping the spirit of the meeting 
alive, ideally with the meeting at about the same time it would have happened 
if the GRC had not been cancelled.

Best wishes Graeme


On 5 Jan 2023, at 14:04, Dekker, Carien 
mailto:carien.dek...@novartis.com>> wrote:

Happy New Year all,

Since I am not at the CCP4 weekend (which is happening right now), I would be 
curious to hear if this is/was discussed and what people think.

Carien

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Frank von Delft
Sent: Monday, December 19, 2022 10:21 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Future Diffraction Methods

This Message is from an External Sender. Do not click links or open attachments 
unless you trust the sender.

Shoot... that sucks.

Yes, we do need something!

"Structural Biology Methods"?


More interesting question:  does it need the GRC to host?  What about 
reimagining the CCP4 study weekend - the question keeps coming up there anyway.

That's one for CCP4 WG1 to discuss - they're meeting straight after New Year, 
so maybe James, you and Ivo should hop on a zoom and kick the idea around.

Frank



On 16/12/2022 22:10, 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://urldefense.com/v3/__https://www.grc.org/about/conference-eval
uation-committee/__;!!N3hqHg43uw!seKRCwqf-9U5a5vpm19quTE94sOBoM1HzktB2
NDBxOp6TFV8LC_s19p5TJcgvxfLfp8BheaUlg1wOfursEBNL8h62_DMr_f2M1U$ )
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 

Re: [ccp4bb] Future Diffraction Methods

[Dekker, Carien]

Happy New Year all,

Since I am not at the CCP4 weekend (which is happening right now), I would be 
curious to hear if this is/was discussed and what people think.

Carien

-Original Message-
From: CCP4 bulletin board  On Behalf Of Frank von Delft
Sent: Monday, December 19, 2022 10:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Future Diffraction Methods

This Message is from an External Sender. Do not click links or open attachments 
unless you trust the sender.

Shoot... that sucks.

Yes, we do need something!

"Structural Biology Methods"?


More interesting question:  does it need the GRC to host?  What about 
reimagining the CCP4 study weekend - the question keeps coming up there anyway.

That's one for CCP4 WG1 to discuss - they're meeting straight after New Year, 
so maybe James, you and Ivo should hop on a zoom and kick the idea around.

Frank



On 16/12/2022 22:10, 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://urldefense.com/v3/__https://www.grc.org/about/conference-eval
> uation-committee/__;!!N3hqHg43uw!seKRCwqf-9U5a5vpm19quTE94sOBoM1HzktB2
> NDBxOp6TFV8LC_s19p5TJcgvxfLfp8BheaUlg1wOfursEBNL8h62_DMr_f2M1U$ ) 
> 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
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC
> .exe?SUBED1=CCP4BB=1__;!!N3hqHg43uw!seKRCwqf-9U5a5vpm19quTE94sOBoM1H
> zktB2NDBxOp6TFV8LC_s19p5TJcgvxfLfp8BheaUlg1wOfursEBNL8h62_DMa7pXohQ$
>
> This message was iss

Re: [ccp4bb] Future Diffraction Methods

[Phoebe A. Rice]

Excellent idea.

From: CCP4 bulletin board  on behalf of Debanu Das 

Date: Saturday, December 24, 2022 at 5:57 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Future Diffraction Methods
Consider merging with the Annual ACA meeting. The ACA meeting can also benefit 
from more X-ray diffraction methods rigor and training and it will help to 
elevate the continuity and history of the ACA and its previous and current 
member participation and contributions in the field.
Best,
Debanu

On Tue, Dec 20, 2022 at 6:40 PM Orville, Allen (DLSLtd,RAL,LSCI) 
<66b6f959eb28-dmarc-requ...@jiscmail.ac.uk<mailto:66b6f959eb28-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Hi,

Thanks James, for organising our last GRC meeting.

In the past few years, I’ve also attended one or more Annual BioXFEL 
International Conferences (open, but ending?) and Ringberg Workshop on Science 
with FELs (by invitation only). Both were excellent meetings held in the 
winter, complemented the GRC in diffraction methods, and benefited from 
relatively small attendance with very focused discussions.  I will also add 
that dynamic structural biology is a rapidly growing area that can include 
simultaneous functional, spectroscopic, and structural data collection from the 
same samples, and using synchrotron, XFEL, and/or electron sources. Moreover, 
many of the other life-science centric GRC’s also include significant 
structural data in their frontier programs and discussions (e.g. metals in 
biology, hemes and tetrapyrroles, enzymes, etc.). We are fundamental to 
biochemistry R… a broad community indeed.

AMO
~ ~ ~ ~ ~
Allen M. Orville, Ph.D.
Wellcome Investigator and Royal Society Wolfson Fellow
Principal Scientist, XFEL Hub at Diamond Light Source
Harwell Science and Innovation Campus
Didcot, Oxfordshire
OX11 0DE
United Kingdom

Phone: +44 (0) 1235 567505
Mobile: +44 (0) 7471 026061
email: allen.orvi...@diamond.ac.uk<mailto:allen.orvi...@diamond.ac.uk>

AMO site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub/Staff/Orville.html
XFEL-Hub site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub.html





From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Frank von Delft 
mailto:frank.vonde...@cmd.ox.ac.uk>>
Date: Monday, 19 December 2022 at 09:22
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Future Diffraction Methods
Shoot... that sucks.

Yes, we do need something!

"Structural Biology Methods"?


More interesting question:  does it need the GRC to host?  What about
reimagining the CCP4 study weekend - the question keeps coming up there
anyway.

That's one for CCP4 WG1 to discuss - they're meeting straight after New
Year, so maybe James, you and Ivo should hop on a zoom and kick the idea
around.

Frank



On 16/12/2022 22:10, 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 de

Re: [ccp4bb] Future Diffraction Methods

[Debanu Das]

Consider merging with the Annual ACA meeting. The ACA meeting can also
benefit from more X-ray diffraction methods rigor and training and it will
help to elevate the continuity and history of the ACA and its previous and
current member participation and contributions in the field.
Best,
Debanu

On Tue, Dec 20, 2022 at 6:40 PM Orville, Allen (DLSLtd,RAL,LSCI) <
66b6f959eb28-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi,
>
>
>
> Thanks James, for organising our last GRC meeting.
>
>
>
> In the past few years, I’ve also attended one or more Annual BioXFEL
> International Conferences (open, but ending?) and Ringberg Workshop on
> Science with FELs (by invitation only). Both were excellent meetings held
> in the winter, complemented the GRC in diffraction methods, and benefited
> from relatively small attendance with very focused discussions.  I will
> also add that dynamic structural biology is a rapidly growing area that can
> include simultaneous functional, spectroscopic, and structural data
> collection from the same samples, and using synchrotron, XFEL, and/or
> electron sources. Moreover, many of the other life-science centric GRC’s
> also include significant structural data in their frontier programs and
> discussions (e.g. metals in biology, hemes and tetrapyrroles, enzymes,
> etc.). We are fundamental to biochemistry R… a broad community indeed.
>
>
>
> AMO
>
> ~ ~ ~ ~ ~
>
> Allen M. Orville, Ph.D.
>
> Wellcome Investigator and Royal Society Wolfson Fellow
>
> Principal Scientist, XFEL Hub at Diamond Light Source
>
> Harwell Science and Innovation Campus
>
> Didcot, Oxfordshire
>
> OX11 0DE
>
> United Kingdom
>
>
>
> Phone: +44 (0) 1235 567505
>
> Mobile: +44 (0) 7471 026061
>
> email: allen.orvi...@diamond.ac.uk
>
>
>
> AMO site:
> https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub/Staff/Orville.html
>
> XFEL-Hub site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub.html
>
>
>
>
>
>
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Frank
> von Delft 
> *Date: *Monday, 19 December 2022 at 09:22
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *Re: [ccp4bb] Future Diffraction Methods
>
> Shoot... that sucks.
>
> Yes, we do need something!
>
> "Structural Biology Methods"?
>
>
> More interesting question:  does it need the GRC to host?  What about
> reimagining the CCP4 study weekend - the question keeps coming up there
> anyway.
>
> That's one for CCP4 WG1 to discuss - they're meeting straight after New
> Year, so maybe James, you and Ivo should hop on a zoom and kick the idea
> around.
>
> Frank
>
>
>
> On 16/12/2022 22:10, 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 bee

Re: [ccp4bb] Future Diffraction Methods

[Orville, Allen (DLSLtd,RAL,LSCI)]

Hi,

Thanks James, for organising our last GRC meeting.

In the past few years, I’ve also attended one or more Annual BioXFEL 
International Conferences (open, but ending?) and Ringberg Workshop on Science 
with FELs (by invitation only). Both were excellent meetings held in the 
winter, complemented the GRC in diffraction methods, and benefited from 
relatively small attendance with very focused discussions.  I will also add 
that dynamic structural biology is a rapidly growing area that can include 
simultaneous functional, spectroscopic, and structural data collection from the 
same samples, and using synchrotron, XFEL, and/or electron sources. Moreover, 
many of the other life-science centric GRC’s also include significant 
structural data in their frontier programs and discussions (e.g. metals in 
biology, hemes and tetrapyrroles, enzymes, etc.). We are fundamental to 
biochemistry R… a broad community indeed.

AMO
~ ~ ~ ~ ~
Allen M. Orville, Ph.D.
Wellcome Investigator and Royal Society Wolfson Fellow
Principal Scientist, XFEL Hub at Diamond Light Source
Harwell Science and Innovation Campus
Didcot, Oxfordshire
OX11 0DE
United Kingdom

Phone: +44 (0) 1235 567505
Mobile: +44 (0) 7471 026061
email: allen.orvi...@diamond.ac.uk

AMO site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub/Staff/Orville.html
XFEL-Hub site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub.html





From: CCP4 bulletin board  on behalf of Frank von Delft 

Date: Monday, 19 December 2022 at 09:22
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Future Diffraction Methods
Shoot... that sucks.

Yes, we do need something!

"Structural Biology Methods"?


More interesting question:  does it need the GRC to host?  What about
reimagining the CCP4 study weekend - the question keeps coming up there
anyway.

That's one for CCP4 WG1 to discuss - they're meeting straight after New
Year, so maybe James, you and Ivo should hop on a zoom and kick the idea
around.

Frank



On 16/12/2022 22:10, 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 f

Re: [ccp4bb] Future Diffraction Methods

[Frank von Delft]

Shoot... that sucks.

Yes, we do need something!

"Structural Biology Methods"?


More interesting question:  does it need the GRC to host?  What about 
reimagining the CCP4 study weekend - the question keeps coming up there 
anyway.


That's one for CCP4 WG1 to discuss - they're meeting straight after New 
Year, so maybe James, you and Ivo should hop on a zoom and kick the idea 
around.


Frank



On 16/12/2022 22:10, 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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[ccp4bb] Future Diffraction Methods

[James Holton]

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



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 
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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Winter, Graeme (DLSLtd,RAL,LSCI)]

he complex is reminiscent of the 
> > carboxylate/BChE complexes observed in crystal structures of hBChE > > 
[Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the > > 
remarkable ability of ChEs to stabilize covalent complexes with carboxylates. > 
> Thus, the study demonstrates that updated processing of older > > diffraction 
images, and the re-refinement of older diffraction data, > > can produce 
valuable information that could not be detected in the > > original analysis, 
and strongly supports the preservation of the > > diffraction images in public 
data banks. > > Best regards > > Joel > > 

 > > Prof. Joel L. Sussman.
joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il>   
www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> > > Dept. of 
Structural Biology   tel: +972  (8) 934 6309   
proteopedia.org<http://proteopedia.org/> > > Weizmann Institute of Science fax: 
+972  (8) 934 6312 > > Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600 > 
> 
-
 > > > > > >> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) > >> 
wrote: > >> > >> Dear Gerard, > >> > >> This is a great idea. Of course I am 
very much in favour of making > >> available raw diffraction images, and such a 
virtual workshop could > >> demonstrate the usefulness of reprocessing raw 
diffraction data and > >> structural refinements. I am not at all afraid that 
archiving of raw > >> data that are the basis of a scientific paper will have 
significant > >> environmental effects: this is minor compared to our everyday 
use of > >> cloud services.  And as Graeme mentioned: when archiving raw data > 
>> make sure to add sufficient and correct meta data. > >> > >> Best wishes, > 
>> Loes > >> > >> ___ > 
>> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> 
Bijvoet Center for Biomolecular Research > >> Utrecht University > >> Padualaan 
8, 3584 CH Utrecht > >> The Netherlands > >> > >> E-mail : 
l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl> > >> phone  : 
+31-30-2532865 > >> fax: +31-30-2533940 > >> > >> Van: CCP4 bulletin board 
namens Gerard > >> Bricogne > >> Verzonden: woensdag 18 maart 2020 23:30 > >> 
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>  > >> Onderwerp: 
[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures > >>   > >> 
Dear colleagues, > >> > >> Perusal and some initial (re-)refinement of the 
various SARS-CoV-2 protease > >> structures in the PDB seems to indicate that 
that there might be potential > >> to improve these if refinements could be 
repeated after some reprocessing > >> and further analysis of the raw 
diffraction images, rather than > >> against the > >> deposited merged data. 
This statement should in no way be construed > >> as a > >> criticism of the 
remarkable achievements of the research groups concerned, > >> who have been 
operating under tremendous time pressure, but as an exciting > >> opportunity 
to push methods to their limits on a uniquely significant class > >> of 
structures. > >> > >> Another consideration is that the various logistical 
problems created by > >> COVID-19 may soon make it increasingly difficult to 
collect new diffraction > >> data on potential drug targets relevant to the 
fight against SARS-CoV-2, > >> underlining the importance of ensuring that the 
best results be obtained > >> from every dataset actually collected, and that 
the most useful conclusions > >> be drawn from the analysis of those datasets 
towards improving the quality > >> of subsequent data collections.  > >> > >> 
On this basis we would like to propose that special efforts be made > >> to 
grant > >> public access to the raw image data associated with any SARS-CoV-2 
related > >> structure that is deposited into the PDB. This can be done by (1) 
archiving > >> these raw image data using resources such as 
data.sbgrid.org<http://data.sbgrid.org/>, zenodo.org<http://zenodo.org/>, > >> 
proteindiffraction.org<http://proteindiffraction.org/> or any other cloud-base

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Winter, Graeme (DLSLtd,RAL,LSCI)]

of. Joel L. Sussman.
joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il>   
www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> > > Dept. of 
Structural Biology   tel: +972  (8) 934 6309   
proteopedia.org<http://proteopedia.org> > > Weizmann Institute of Science fax: 
+972  (8) 934 6312 > > Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600 > 
> 
-
 > > > > > >> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) > >> 
wrote: > >> > >> Dear Gerard, > >> > >> This is a great idea. Of course I am 
very much in favour of making > >> available raw diffraction images, and such a 
virtual workshop could > >> demonstrate the usefulness of reprocessing raw 
diffraction data and > >> structural refinements. I am not at all afraid that 
archiving of raw > >> data that are the basis of a scientific paper will have 
significant > >> environmental effects: this is minor compared to our everyday 
use of > >> cloud services.  And as Graeme mentioned: when archiving raw data > 
>> make sure to add sufficient and correct meta data. > >> > >> Best wishes, > 
>> Loes > >> > >> ___ > 
>> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> 
Bijvoet Center for Biomolecular Research > >> Utrecht University > >> Padualaan 
8, 3584 CH Utrecht > >> The Netherlands > >> > >> E-mail : 
l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl> > >> phone  : 
+31-30-2532865 > >> fax: +31-30-2533940 > >> > >> Van: CCP4 bulletin board 
namens Gerard > >> Bricogne > >> Verzonden: woensdag 18 maart 2020 23:30 > >> 
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>  > >> Onderwerp: 
[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures > >>   > >> 
Dear colleagues, > >> > >> Perusal and some initial (re-)refinement of the 
various SARS-CoV-2 protease > >> structures in the PDB seems to indicate that 
that there might be potential > >> to improve these if refinements could be 
repeated after some reprocessing > >> and further analysis of the raw 
diffraction images, rather than > >> against the > >> deposited merged data. 
This statement should in no way be construed > >> as a > >> criticism of the 
remarkable achievements of the research groups concerned, > >> who have been 
operating under tremendous time pressure, but as an exciting > >> opportunity 
to push methods to their limits on a uniquely significant class > >> of 
structures. > >> > >> Another consideration is that the various logistical 
problems created by > >> COVID-19 may soon make it increasingly difficult to 
collect new diffraction > >> data on potential drug targets relevant to the 
fight against SARS-CoV-2, > >> underlining the importance of ensuring that the 
best results be obtained > >> from every dataset actually collected, and that 
the most useful conclusions > >> be drawn from the analysis of those datasets 
towards improving the quality > >> of subsequent data collections.  > >> > >> 
On this basis we would like to propose that special efforts be made > >> to 
grant > >> public access to the raw image data associated with any SARS-CoV-2 
related > >> structure that is deposited into the PDB. This can be done by (1) 
archiving > >> these raw image data using resources such as 
data.sbgrid.org<http://data.sbgrid.org>, zenodo.org<http://zenodo.org>, > >> 
proteindiffraction.org<http://proteindiffraction.org> or any other cloud-based 
data-sharing service, and > >> (2) communicating the corresponding DOIs to the 
wwPDB centres. This idea > >> could be extended to datasets that investigators 
would like to offer to > >> interested methods developers or expert users at 
the pre-deposition stage. > >> > >> Experts making use of those raw data would 
be encouraged to document, > >> in as > >> much detail as possible, how 
particular programs or workflows could > >> be used > >> on those 
structures/datasets to obtain the best results. This would > >> be a > >> kind 
of "virtual workshop", a particularly valuable collective > >> activity at > >> 
the present time when several in-

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[John Berrisford]

aw diffraction images, and such a 
virtual workshop could > >> demonstrate the usefulness of reprocessing raw 
diffraction data and > >> structural refinements. I am not at all afraid that 
archiving of raw > >> data that are
  the bas
is of a scientific paper will have significant > >> environmental effects: this 
is minor compared to our everyday use of > >> cloud services. And as Graeme 
mentioned: when archiving raw data > >> make sure to add sufficient and correct 
meta data. > >> > >> Best wishes, > >> Loes > >> > >> 
___________ > >> Dr. Loes 
Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> Bijvoet 
Center for Biomolecular Research > >> Utrecht University > >> Padualaan 8, 3584 
CH Utrecht > >> The Netherlands > >> > >> E-mail : l.m.j.kroon-batenb...@uu.nl 
> >> phone : +31-30-2532865 > >> fax : +31-30-2533940 > >> > >> Van: CCP4 
bulletin board namens Gerard > >> Bricogne > >> Verzonden: woensdag 18 maart 
2020 23:30 > >> Aan: CCP4BB@JISCMAIL.AC.UK > >> Onderwerp: [ccp4bb] Raw 
diffraction images for SARS-CoV-2 related structures > >> > >> Dear colleagues, 
> >> > >> Perusal and some initial (re-)refinement of the various SARS-CoV-2 
protease > 
 >> struc
tures in the PDB seems to indicate that that there might be potential > >> to 
improve these if refinements could be repeated after some reprocessing > >> and 
further analysis of the raw diffraction images, rather than > >> against the > 
>> deposited merged data. This statement should in no way be construed > >> as 
a > >> criticism of the remarkable achievements of the research groups 
concerned, > >> who have been operating under tremendous time pressure, but as 
an exciting > >> opportunity to push methods to their limits on a uniquely 
significant class > >> of structures. > >> > >> Another consideration is that 
the various logistical problems created by > >> COVID-19 may soon make it 
increasingly difficult to collect new diffraction > >> data on potential drug 
targets relevant to the fight against SARS-CoV-2, > >> underlining the 
importance of ensuring that the best results be obtained > >> from every 
dataset actually collected, and that the most useful conclusions > >> be dr
 awn from
 the analysis of those datasets towards improving the quality > >> of 
subsequent data collections. > >> > >> On this basis we would like to propose 
that special efforts be made > >> to grant > >> public access to the raw image 
data associated with any SARS-CoV-2 related > >> structure that is deposited 
into the PDB. This can be done by (1) archiving > >> these raw image data using 
resources such as data.sbgrid.org, zenodo.org, > >> proteindiffraction.org or 
any other cloud-based data-sharing service, and > >> (2) communicating the 
corresponding DOIs to the wwPDB centres. This idea > >> could be extended to 
datasets that investigators would like to offer to > >> interested methods 
developers or expert users at the pre-deposition stage. > >> > >> Experts 
making use of those raw data would be encouraged to document, > >> in as > >> 
much detail as possible, how particular programs or workflows could > >> be 
used > >> on those structures/datasets to obtain the best results. This w
 ould > >
> be a > >> kind of "virtual workshop", a particularly valuable collective > >> 
> activity at > >> the present time when several in-person workshops (e.g. 
> RapiData) > >> have been > >> cancelled and many meetings are in limbo for 
> several months. > >> > >> The latter activity would benefit from having a 
> centralised facility > >> set up > >> for the experts to post their results 
> and annotations: we could > >> create such > >> a facility, but other, larger 
> groups might want to consider doing so. > >> > >> > >> With best wishes, > >> 
> > >> Clemens & Gerard. > >> > >> 
>  > >> 
> > >> 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 > > > > > > To 
> unsubscribe from the CCP4BB list, click the following l
 ink: > >
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > 
 > > To 
unsubscribe from the CCP4BB list, click the following link: > 
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[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Gerard Bricogne]

Dear all,

 It is a pleasure to be able to end the (GMT) week by calling for a huge
round of applause for the Diamond team, who this afternoon started uploading
a large collection of sets of raw diffraction images (77 as we write but the
upload is still ongoing) for PDB entries that were released two days ago.

 Special thanks to Graeme Winter who organised the upload to Zenodo. The
datasets are collectively accessible via the following link:

https://zenodo.org/search?page=1=20=keywords:%22SARS-CoV-2%20main%20protease%22

 Graeme asked that "major kudos [be given] to Zenodo developers who have
been very responsive with helping us do automated downloads".

 Happy scrutiny and reprocessing of these datasets, and re-refinement of
the associated structures, to all hard-core MX addicts!


 With best wishes,

 Clemens & Gerard.

--
On Thu, Mar 19, 2020 at 10:00:11AM +, John Berrisford wrote:
> Dear all
> 
> The wwPDB OneDep system allows depositors to provide DOIs of raw
> diffraction images during deposition to the PDB and once again
> encourages depositors to provide a DOI for raw images when they have
> submitted.  
> 
> Out of the 9665 X-ray entries that were released in 2019 we have DOI's
> for raw images in 205 of these entries.  
> 
> We would encourage depositors to provide the DOI for their raw images
> when they are available.  
> 
> Regards
> 
> John
> 
> 
> On Mar 19 2020, at 9:48 am, Joel Sussman  wrote:
> 
> > 19-Mar-2020
> > Dear Loes, Peter, Clemens & Gerard,
> > I concur that it is crucial to preserve the original diffraction data
> > and make it available to anyone who would like to use it.
> > As an example, please see the very recent paper by 
> > Nachon et al (2020). "A second look at the crystal structures of
> > Drosophila melanogaster acetylcholinesterase in complex with tacrine
> > derivatives provides Insights concerning catalytic intermediates and
> > the design of specific insecticides" Molecules 25 pii: E1198 
> > [https://www.ncbi.nlm.nih.gov/pubmed/32155891].
> > The study reexamines the original data, with modern software tools,
> > the original data of a paper we published in 2000 (~20 years ago) and
> > revealed features that had not been noticed. Specifically 
> > 1) previously unmodeled density in the native active site can be
> > interpreted as stable acetylation of the catalytic serine. 
> > 2) Similarly, a strong density in the DmAChE/ZA complex, originally
> > attributed to a sulfate ion, is better interpreted as a small molecule
> > that is covalently bound. The complex is reminiscent of the
> > carboxylate/BChE complexes observed in crystal structures of hBChE
> > [Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the
> > remarkable ability of ChEs to stabilize covalent complexes with 
> > carboxylates.
> > Thus, the study demonstrates that updated processing of older
> > diffraction images, and the re-refinement of older diffraction data,
> > can produce valuable information that could not be detected in the
> > original analysis, and strongly supports the preservation of the
> > diffraction images in public data banks.
> > Best regards
> > Joel
> > 
> > Prof. Joel L. Sussman.        joel.suss...@weizmann.ac.il   
> > www.weizmann.ac.il/~joel
> > Dept. of Structural Biology   tel: +972  (8) 934 6309       proteopedia.org
> > Weizmann Institute of Science fax: +972  (8) 934 6312
> > Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
> > -
> >  
> >  
> >> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
> >>  wrote:
> >>  
> >> Dear Gerard,
> >>  
> >> This is a great idea. Of course I am very much in favour of making
> >> available raw diffraction images, and such a virtual workshop could
> >> demonstrate the usefulness of reprocessing raw diffraction data and
> >> structural refinements. I am not at all afraid that archiving of raw
> >> data that are the basis of a scientific paper will have significant
> >> environmental effects: this is minor compared to our everyday use of
> >> cloud services.  And as Graeme mentioned: when archiving raw data
> >> make sure to add sufficient and correct meta data.
> >>  
> >> Best wishes,
> >> Loes
> >>  
> >> ___
> >> Dr. Loes Kroon-Batenburg
> >> Dept. of C

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Clemens Vonrhein]

Dear all,

as a follow-up to our initial message (and similar to other activities
from the MX community), we added some content to our BUSTER wiki at

  https://www.globalphasing.com/buster/wiki/index.cgi?Covid19

to show interested users how to (re-)refine existing PDB entries with
BUSTER and how to look at the results. For anyone wanting to
(re-)process deposited raw diffraction data, we've started a page on
the autoPROC wiki at

  https://www.globalphasing.com/autoproc/wiki/index.cgi?RevisitingExistingData

that might be useful.

We will keep adding and updating those pages over the next days,
especially if more raw diffraction data becomes available and/or more
PDB structures are deposited or becoming relevant. We are very
grateful to any researcher making their (raw) data available under
such pressure and stress!

If there are any questions, suggestions, requests or ideas: please let
us know.

Best regards

Clemens & Gerard



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Ivan Shabalin]

Dear All,

A short note about https://proteindiffraction.org/:

If you upload images for an already deposited structure, you dont need 
to update your PDB entry to provide the DOI. PDB and 
proteindiffraction.org communicate on a regular basis to link entries to 
datasets.


Ivan



With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 3/19/20 06:00, John Berrisford wrote:

Dear all

The wwPDB OneDep system allows depositors to provide DOIs of raw
diffraction images during deposition to the PDB and once again
encourages depositors to provide a DOI for raw images when they have
submitted.

Out of the 9665 X-ray entries that were released in 2019 we have DOI's
for raw images in 205 of these entries.

We would encourage depositors to provide the DOI for their raw images
when they are available.

Regards

John


On Mar 19 2020, at 9:48 am, Joel Sussman  wrote:


19-Mar-2020
Dear Loes, Peter, Clemens & Gerard,
I concur that it is crucial to preserve the original diffraction data
and make it available to anyone who would like to use it.
As an example, please see the very recent paper by
Nachon et al (2020). "A second look at the crystal structures of
Drosophila melanogaster acetylcholinesterase in complex with tacrine
derivatives provides Insights concerning catalytic intermediates and
the design of specific insecticides" Molecules 25 pii: E1198
[https://www.ncbi.nlm.nih.gov/pubmed/32155891].
The study reexamines the original data, with modern software tools,
the original data of a paper we published in 2000 (~20 years ago) and
revealed features that had not been noticed. Specifically
1) previously unmodeled density in the native active site can be
interpreted as stable acetylation of the catalytic serine.
2) Similarly, a strong density in the DmAChE/ZA complex, originally
attributed to a sulfate ion, is better interpreted as a small molecule
that is covalently bound. The complex is reminiscent of the
carboxylate/BChE complexes observed in crystal structures of hBChE
[Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the
remarkable ability of ChEs to stabilize covalent complexes with carboxylates.
Thus, the study demonstrates that updated processing of older
diffraction images, and the re-refinement of older diffraction data,
can produce valuable information that could not be detected in the
original analysis, and strongly supports the preservation of the
diffraction images in public data banks.
Best regards
Joel

Prof. Joel L. Sussman.        joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309       proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
-
  
  

On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
 wrote:
  
Dear Gerard,
  
This is a great idea. Of course I am very much in favour of making

available raw diffraction images, and such a virtual workshop could
demonstrate the usefulness of reprocessing raw diffraction data and
structural refinements. I am not at all afraid that archiving of raw
data that are the basis of a scientific paper will have significant
environmental effects: this is minor compared to our everyday use of
cloud services.  And as Graeme mentioned: when archiving raw data
make sure to add sufficient and correct meta data.
  
Best wishes,

Loes
  
___

Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands
  
E-mail : l.m.j.kroon-batenb...@uu.nl

phone  : +31-30-2532865
fax    : +31-30-2533940
  
Van: CCP4 bulletin board  namens Gerard

Bricogne 
Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK 
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
  
Dear colleagues,
  
Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease

structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than
against the
deposited merged data. This statement should in no way be construed
as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.
  
Another consideration is th

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Filipe Maia]

Dear Colleagues,

I would like to add my voice to those advocating making available raw
diffraction images and point out another resource for raw data deposition,
https://cxidb.org, particularly for the case of emerging methods such as
serial crystallography.

Cheers,
Filipe

On Thu, 19 Mar 2020 at 09:01, Clemens Vonrhein 
wrote:

> Dear Petr,
>
> On Thu, Mar 19, 2020 at 06:45:31AM +, Petr Kolenko wrote:
> > For those of you who are in touch with these data, would deposition
> > of unmerged intensities in P1 in the whole detector range instead of
> > complete dataset be good enough to „correctly“ re-evaluete the
> > structure? Or is there a doubt that even this approach would not
> > lead to optimal structure?
>
> It would be a step in the right direction, yes ... but:
>
>  * It assumes that all spots have been integrated and nothing else
>than those spots: there can be cases of missed unit cell
>duplications or incorrect enforcement of a unit cell and symmetry
>(because those crystals always come in a known cell/SG, right?).
>
>  * We'll still be stuck with a particular intergration program and a
>particular set of user decisions how to run it. Yes, all modern
>data processing programs and packages are usually doing a great job
>if run in (more or less) default mode on (more or less) good
>crystals. But not everything is lysozyme/thaumatin/XYZ collected
>fine-sliced on a PAD with low-dose, high-multiplicity on a well
>calibrated instrument ;-)
>
>  * If integration was done in P1 the cell parameter restraints of the
>(potentiually different) true SG were not enforced - which can lead
>to incorrect cell parameters (which has knock-on effects in
>refinement ... remember the WhatIf check for correct cell
>parameter?).
>
>If integration was done in a non-P1 SG and that choice was
>incorrect: how do we know that those cell parameters didn't enforce
>an incorrect set of cell parameter restraints, leading to poor
>integration? Again: different programs have different ways of
>assigning pixels (and their counts) to a reflection intensity
>(concepts like shoebox, profile-fitting, pixel-labeling etc all
>come to mind).
>
>  * Integration itself can be suboptimal if there are issues with the
>crystal (ice rings, split, multiple lattices etc), the instrument
>(damaged pixels, beam jitter, incorrect countrate cut-off handling
>etc) or the experiment (radiation damage etc). Data processing
>defaults might not always work correctly/best for all cases.
>
>  * The raw images allow such corrections (damaged pixels not yet in
>pixel mask, incorrect handling of countrate_cutoff) and additional
>analysis (e.g. radiation damage analysis a la F(early)-F(late) maps
>[1]).
>
> So the raw integrated (not scaled/corrected) and unmerged intensities
> might indeed often be good enough, but if we are going to try and
> deposit more than just the merged and scaled intensities/amplitudes
> (as we do now) - and this will involve additional work and change from
> our side - then why not bite the bullet once and try to go all the way
> to raw images:
>
>   * The infrastructure is already in place (proteindiffraction.org,
> data.sbgrid.org, zenodo.org, wwPDB DOIs, etc), ready for use right
> now.
>
>   * From experience at multiple worshops: everyone is comfortable to
> start data processing from raw images using the various software
> tools out there that people are familiar with (while jumping in
> half way is probably more challenging to non power-users).
>
> Anyway, just some ideas - from someone downloading nearly all deposited
> raw image data on a regular basis for testing and developing data
> processing software (and finding a lot of issues in our software this
> way ... as well as issues with experiments and sometimes the
> instrument).
>
> Cheers
>
> Clemens
>
> [1] as e.g. done in autoPROC+BUSTER
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Harry Powell - CCP4BB]

Hi

> While those text files would be heavy, they'd be still lighter than raw 
> images and the whole useless white space they carry with them between 
> reflections.

At the risk of extending this thread into a different direction, the "white 
space (the images) carry with them between reflections” is only useless because 
we (the developers of integration software and structural biologists who use 
X-ray diffraction) choose to throw it away. The same as the can that surrounds 
my beans in tomato sauce...

There are plenty of people out there who have proposed using the non-Bragg 
scattering (aka “diffuse scattering”, inter alia) to give extra structural 
information.

My two ha’porth…

Harry

> On 19 Mar 2020, at 08:47, Julien Cappèle  
> wrote:
> 
> Hi everyone,
> 
> There are some very interesting ideas. 
> 
> Though I agree with you Clement that raw images are amazing to work with as 
> you can use any software you are confortable with, we cannot forget that 
> depositing several TB of data for each lab would be bad for ecological 
> reason. And because detectors are always improving (thank you all!), size of 
> data will increase exponentially. 
> 
> Correct me if I'm wrong, as I am not that familiar with the way that 
> integration of raw images works:
> 
> Could it be possible for a new/already existing software to store reflections 
> (area, intensity from center to border, position x/y on the image, and 
> information of the image) in a lightweight and text only file ? Possibly a 
> new format to be used for integration ?
> 
> While those text files would be heavy, they'd be still lighter than raw 
> images and the whole useless white space they carry with them between 
> reflections.
> 
> If not possible, could we imagine to eliminate all the unused space on these 
> ? Like a super raw image diet-plan for the incoming summer !
> 
> Best regards,
> 
> Julien CAPPELE
> Université de Lorraine, Nancy, France
> PhD student - 2nd Year
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Andreas Förster]

This last, very important point made by Graeme gives me the chance to plug
a satellite workshop at the IUCr Congress (end of August, so fingers
crossed that this will go ahead) on "MX raw image data formats, metadata
and validation".  This is organized by Herbert Bernstein, Loes
Kroon-Batenburg, Brian McMahon and myself, and will take place on 22 Aug
from morning till 3 pm.

Why is this relevant?  Over the past few years, many beamline scientists
from synchrotrons (and XFELs) the world over have worked hard to turn the
perception of a lack of metadata into a transcription of essential metadata
items in a language that can be saved with current data formats (HDF5 and
CBF), can be used for archiving and retrieval of data, and is understood by
automatic processing pipelines.  We like to call this the Gold Standard.
The Gold Standard demands the beam center is recorded for every
experiment.  It also insists on synchrotron and beamline, items that are
curiously absent from a lot of datasets.  In the Gold Standard, you'll find
a full description of the diffraction experiment and won't have to guess
anymore what the rotation axis is and how the detector is positioned.

The purpose of the Prague workshop is to make the Gold Standard better
known to a wider audience, explain what's in it and how different
synchrotrons are applying it, and discuss how to expand this to chemical
crystallography.  The program is still a work in progress and the website
rather austere (
https://www.iucr.org/resources/data/commdat/prague-workshop-mx-raw-data),
but mark your calendars if you're interested.  We'll have a great line-up
of speakers and ample opportunity for discussions.  As the workshop will
take place in the conference center, it will be only a short walk to the
opening ceremony later that day.

All best.


Andreas (wearing my DECTRIS hat).



On Thu, Mar 19, 2020 at 10:08 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Hi Folks,
>
> Quick note on "Like a super raw image diet-plan for the incoming summer” -
> the bslz4 compression used with Eiger works really well, and the data are
> pretty close to entropy limit in terms of size - which means if you measure
> your data carefully (i.e. low background etc.) you can realistically have a
> full Eiger data set which will fit on a DVD -
>
> Grey-Area i04-ins :) $ du -ach insu_d200_1*h5
> 2.5Ginsu_d200_1_01.h5
> 1.9Ginsu_d200_1_02.h5
>  92Kinsu_d200_1_master.h5
> 138Minsu_d200_1_meta.h5
> 4.0Kinsu_d200_1_meta_pack.h5
> 4.5Gtotal
>
> which I think is pretty modest storage wise - this is 1,800 image Eiger
> 16M data set so pretty realistic.
>
> No matter how much data we produce, the particle physicists have us beat,
> and I would wager that netflix is a couple of orders of magnitude worse
> than MX for the environment.
>
> Also, it costs a lot more CO2 to produce the data than to store it -
> synchrotrons don’t run on wind turbines ;-)
>
> I agree with Clemens - if we are serious about revisiting the data, you
> have to have access to the actual data rather than a description of the
> data (which is essentially what an MTZ file is)
>
> A small administrative note for those uploading to zenodo etc -
>
> if you are uploading HDF5 as above, this works fine
> if you are uploading CBF images, would suggest you gzip / bzip2 compress
> them (pick one) and then tar up each sweep independently before upload
>
>  - makes fetching the data back down again efficient. Zenodo does not do
> well with many many small files (I have discussed this with the zenodo
> developers - it is a reasonable design choice)
>
> Finally I would ask if you do upload raw data please also upload the
> beamline parameters you used e.g. the beam centre from a white board or
> whatever - if it’s not in the headers it is not known
>
> All the best Graeme
>
> > On 19 Mar 2020, at 08:47, Julien Cappèle <
> julien.capp...@univ-lorraine.fr> wrote:
> >
> > Hi everyone,
> >
> > There are some very interesting ideas.
> >
> > Though I agree with you Clement that raw images are amazing to work with
> as you can use any software you are confortable with, we cannot forget that
> depositing several TB of data for each lab would be bad for ecological
> reason. And because detectors are always improving (thank you all!), size
> of data will increase exponentially.
> >
> > Correct me if I'm wrong, as I am not that familiar with the way that
> integration of raw images works:
> >
> > Could it be possible for a new/already existing software to store
> reflections (area, intensity from center to border, position x/y on the
> image, and information of the image) in a lightweight and text only file ?
> Possibly a new format to be used for integration ?
> >
> > While those text files would be heavy, they'd be still lighter than raw
> images and the whole useless white space they carry with them between
> reflections.
> >
> > If not possible, could we imagine to eliminate all 

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[John Berrisford]

Dear all

The wwPDB OneDep system allows depositors to provide DOIs of raw
diffraction images during deposition to the PDB and once again
encourages depositors to provide a DOI for raw images when they have
submitted.  

Out of the 9665 X-ray entries that were released in 2019 we have DOI's
for raw images in 205 of these entries.  

We would encourage depositors to provide the DOI for their raw images
when they are available.  

Regards

John


On Mar 19 2020, at 9:48 am, Joel Sussman  wrote:

> 19-Mar-2020
> Dear Loes, Peter, Clemens & Gerard,
> I concur that it is crucial to preserve the original diffraction data
> and make it available to anyone who would like to use it.
> As an example, please see the very recent paper by 
> Nachon et al (2020). "A second look at the crystal structures of
> Drosophila melanogaster acetylcholinesterase in complex with tacrine
> derivatives provides Insights concerning catalytic intermediates and
> the design of specific insecticides" Molecules 25 pii: E1198 
> [https://www.ncbi.nlm.nih.gov/pubmed/32155891].
> The study reexamines the original data, with modern software tools,
> the original data of a paper we published in 2000 (~20 years ago) and
> revealed features that had not been noticed. Specifically 
> 1) previously unmodeled density in the native active site can be
> interpreted as stable acetylation of the catalytic serine. 
> 2) Similarly, a strong density in the DmAChE/ZA complex, originally
> attributed to a sulfate ion, is better interpreted as a small molecule
> that is covalently bound. The complex is reminiscent of the
> carboxylate/BChE complexes observed in crystal structures of hBChE
> [Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the
> remarkable ability of ChEs to stabilize covalent complexes with carboxylates.
> Thus, the study demonstrates that updated processing of older
> diffraction images, and the re-refinement of older diffraction data,
> can produce valuable information that could not be detected in the
> original analysis, and strongly supports the preservation of the
> diffraction images in public data banks.
> Best regards
> Joel
> 
> Prof. Joel L. Sussman.        joel.suss...@weizmann.ac.il   
> www.weizmann.ac.il/~joel
> Dept. of Structural Biology   tel: +972  (8) 934 6309       proteopedia.org
> Weizmann Institute of Science fax: +972  (8) 934 6312
> Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
> -
>  
>  
>> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
>>  wrote:
>>  
>> Dear Gerard,
>>  
>> This is a great idea. Of course I am very much in favour of making
>> available raw diffraction images, and such a virtual workshop could
>> demonstrate the usefulness of reprocessing raw diffraction data and
>> structural refinements. I am not at all afraid that archiving of raw
>> data that are the basis of a scientific paper will have significant
>> environmental effects: this is minor compared to our everyday use of
>> cloud services.  And as Graeme mentioned: when archiving raw data
>> make sure to add sufficient and correct meta data.
>>  
>> Best wishes,
>> Loes
>>  
>> ___
>> Dr. Loes Kroon-Batenburg
>> Dept. of Crystal and Structural Chemistry
>> Bijvoet Center for Biomolecular Research
>> Utrecht University
>> Padualaan 8, 3584 CH Utrecht
>> The Netherlands
>>  
>> E-mail : l.m.j.kroon-batenb...@uu.nl
>> phone  : +31-30-2532865
>> fax    : +31-30-2533940
>>  
>> Van: CCP4 bulletin board  namens Gerard
>> Bricogne 
>> Verzonden: woensdag 18 maart 2020 23:30
>> Aan: CCP4BB@JISCMAIL.AC.UK 
>> Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
>>  
>> Dear colleagues,
>>  
>> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
>> structures in the PDB seems to indicate that that there might be potential
>> to improve these if refinements could be repeated after some reprocessing
>> and further analysis of the raw diffraction images, rather than
>> against the
>> deposited merged data. This statement should in no way be construed
>> as a
>> criticism of the remarkable achievements of the research groups concerned,
>> who have been operating under tremendous time pressure, but as an exciting
>> opportunity to push methods to their limits on a uniquely significant class
>> of structures.
>>  
>> Another consideration i

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Joel Sussman]

  19-Mar-2020
Dear Loes, Peter, Clemens & Gerard,
I concur that it is crucial to preserve the original diffraction data and make 
it available to anyone who would like to use it.
As an example, please see the very recent paper by
Nachon et al (2020). "A second look at the crystal structures of Drosophila 
melanogaster acetylcholinesterase in complex with tacrine derivatives provides 
Insights concerning catalytic intermediates and the design of specific 
insecticides" Molecules 25 pii: E1198
[https://www.ncbi.nlm.nih.gov/pubmed/32155891].
The study reexamines the original data, with modern software tools, the 
original data of a paper we published in 2000 (~20 years ago) and revealed 
features that had not been noticed. Specifically
1) previously unmodeled density in the native active site can be interpreted as 
stable acetylation of the catalytic serine.
2) Similarly, a strong density in the DmAChE/ZA complex, originally attributed 
to a sulfate ion, is better interpreted as a small molecule that is covalently 
bound. The complex is reminiscent of the carboxylate/BChE complexes observed in 
crystal structures of hBChE [Brazzolotto et al, 2012; Nicolet et al, 2003], and 
demonstrates the remarkable ability of ChEs to stabilize covalent complexes 
with carboxylates.
Thus, the study demonstrates that updated processing of older diffraction 
images, and the re-refinement of older diffraction data, can produce valuable 
information that could not be detected in the original analysis, and strongly 
supports the preservation of the diffraction images in public data banks.
Best regards
Joel

Prof. Joel L. Sussman.
joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il>   
www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel>
Dept. of Structural Biology   tel: +972  (8) 934 6309   
proteopedia.org<http://proteopedia.org>
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) 
mailto:l.m.j.kroon-batenb...@uu.nl>> wrote:

Dear Gerard,

This is a great idea. Of course I am very much in favour of making available 
raw diffraction images, and such a virtual workshop could demonstrate the 
usefulness of reprocessing raw diffraction data and structural refinements. I 
am not at all afraid that archiving of raw data that are the basis of a 
scientific paper will have significant environmental effects: this is minor 
compared to our everyday use of cloud services.  And as Graeme mentioned: when 
archiving raw data make sure to add sufficient and correct meta data.

Best wishes,
Loes

___
Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands

E-mail : l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl>
phone  : +31-30-2532865
fax: +31-30-2533940


Van: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
namens Gerard Bricogne mailto:g...@globalphasing.com>>
Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as 
da

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Clemens Vonrhein]

Dear Julien,

On Thu, Mar 19, 2020 at 08:47:20AM +, Julien Cappèle wrote:
> Though I agree with you Clemens that raw images are amazing to work
> with as you can use any software you are confortable with, we cannot
> forget that depositing several TB of data for each lab would be bad
> for ecological reason.

Of course, there are ecological (carbon footprint) considerations -
and there are lots of papers and studies about that. I haven't looked
at any numbers, but maybe some points:

 * A lot of data is already stored (e.g. at synchrotrons) and would
   "only" needed to be made "visible" via a DOI (caveat: I realise
   that there are huge technical issues with that)

 * How does that energy consumption compare with the energy used to
   perform the experiment in the first place?

 * If by having that data available we can improve software and the
   way experiments are done: wouldn't that potentially save energy in
   hte long run (avoiding poor or unnecessary experiments in the first
   place)?

 * We are looking at a move to increase the number of raw image data
   depositions for deposited PDB structures - not at a requirement to
   deposit raw images for every PDB structure or even for every
   dataset ever collected.

   At the moment there are about 4500 image datasets available for
   about 10 PDB X-Ray structures, i.e. ~5%. 

> And because detectors are always improving (thank you all!), size of
> data will increase exponentially.

True ... and some type of experiment can benefit from those larger,
faster and more numerous types of datasets - if done correctly.

> Could it be possible for a new/already existing software to store
> reflections (area, intensity from center to border, position x/y on
> the image, and information of the image) in a lightweight and text
> only file ? Possibly a new format to be used for integration ?

See my other reply: this all assumes that the initial processing step
caught all spots (and nothing else) on the 2D image correctly.

There have been all kind of initiatives about raw data deposition (in
no particular order)

  https://www.iucr.org/resources/data/dddwg
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5331468/
  https://www.sciencedaily.com/releases/2016/11/161108130045.htm
  https://journals.iucr.org/d/issues/2016/11/00/yt5099/
  https://onlinelibrary.wiley.com/iucr/doi/10.1107/S0909049513020724
  http://scripts.iucr.org/cgi-bin/paper?S0907444908015540
  https://scripts.iucr.org/cgi-bin/paper?dz5309
  https://bl831.als.lbl.gov/~jamesh/lossy_compression/

So we've been there before. Let's see if we can't do at least
something for the clearly important structures and work right now -
and worry about some long-term impact later (having maybe learned
something along the way). Just because we could be doing something now
doesn't mean we will have to keep doing this in a 1-N years time,
right ;-)

Cheers

Clemens



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Peter Keller]

Dear all,

On Thu, 19 Mar 2020, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:


Date: Thu, 19 Mar 2020 09:08:21
From: "Winter, Graeme (DLSLtd,RAL,LSCI)" 
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures



No matter how much data we produce, the particle physicists have us beat, 
and I would wager that netflix is a couple of orders of magnitude worse 
than MX for the environment.


And not only the particle physicists - the astronomers too. A few years ago, 
I came across a figure for the daily data output rate of one of the projects 
that scans observatory data for objects that might be on a collision course 
with the Earth. We are a drop in the ocean in comparison.


Anyway, whatever the balance of opinion on long-term archiving of raw image 
data, that is not the issue that Gerard and Clemens have raised. It is 
rather making raw data available to the maximum number of researchers on a 
massively important and urgent question of pubic health. It is in the same 
spirit as the sequence of SARS-CoV-2 having been made immediately available 
by the Chinese researchers who first obtained it. I think that the case for 
doing so where there are no major technical impediments is unanswerable.


Regards,
Peter.


--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Kroon-Batenburg, L.M.J. (Loes)]

Dear Gerard,

This is a great idea. Of course I am very much in favour of making available 
raw diffraction images, and such a virtual workshop could demonstrate the 
usefulness of reprocessing raw diffraction data and structural refinements. I 
am not at all afraid that archiving of raw data that are the basis of a 
scientific paper will have significant environmental effects: this is minor 
compared to our everyday use of cloud services.  And as Graeme mentioned: when 
archiving raw data make sure to add sufficient and correct meta data.

Best wishes,
Loes


___

Dr. Loes Kroon-Batenburg

Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands

E-mail : l.m.j.kroon-batenb...@uu.nl
phone  : +31-30-2532865
fax: +31-30-2533940


Van: CCP4 bulletin board  namens Gerard Bricogne 

Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK 
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as data.sbgrid.org, zenodo.org,
proteindiffraction.org or any other cloud-based data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.

Experts making use of those raw data would be encouraged to document, in as
much detail as possible, how particular programs or workflows could be used
on those structures/datasets to obtain the best results. This would be a
kind of "virtual workshop", a particularly valuable collective activity at
the present time when several in-person workshops (e.g. RapiData) have been
cancelled and many meetings are in limbo for several months.

The latter activity would benefit from having a centralised facility set up
for the experts to post their results and annotations: we could create such
a facility, but other, larger groups might want to consider doing so.


With best wishes,

Clemens & Gerard.



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi Folks,

Quick note on "Like a super raw image diet-plan for the incoming summer” - the 
bslz4 compression used with Eiger works really well, and the data are pretty 
close to entropy limit in terms of size - which means if you measure your data 
carefully (i.e. low background etc.) you can realistically have a full Eiger 
data set which will fit on a DVD -

Grey-Area i04-ins :) $ du -ach insu_d200_1*h5
2.5Ginsu_d200_1_01.h5
1.9Ginsu_d200_1_02.h5
 92Kinsu_d200_1_master.h5
138Minsu_d200_1_meta.h5
4.0Kinsu_d200_1_meta_pack.h5
4.5Gtotal

which I think is pretty modest storage wise - this is 1,800 image Eiger 16M 
data set so pretty realistic. 

No matter how much data we produce, the particle physicists have us beat, and I 
would wager that netflix is a couple of orders of magnitude worse than MX for 
the environment. 

Also, it costs a lot more CO2 to produce the data than to store it - 
synchrotrons don’t run on wind turbines ;-)  

I agree with Clemens - if we are serious about revisiting the data, you have to 
have access to the actual data rather than a description of the data (which is 
essentially what an MTZ file is) 

A small administrative note for those uploading to zenodo etc - 

if you are uploading HDF5 as above, this works fine
if you are uploading CBF images, would suggest you gzip / bzip2 compress them 
(pick one) and then tar up each sweep independently before upload

 - makes fetching the data back down again efficient. Zenodo does not do well 
with many many small files (I have discussed this with the zenodo developers - 
it is a reasonable design choice) 

Finally I would ask if you do upload raw data please also upload the beamline 
parameters you used e.g. the beam centre from a white board or whatever - if 
it’s not in the headers it is not known 

All the best Graeme

> On 19 Mar 2020, at 08:47, Julien Cappèle  
> wrote:
> 
> Hi everyone,
> 
> There are some very interesting ideas. 
> 
> Though I agree with you Clement that raw images are amazing to work with as 
> you can use any software you are confortable with, we cannot forget that 
> depositing several TB of data for each lab would be bad for ecological 
> reason. And because detectors are always improving (thank you all!), size of 
> data will increase exponentially. 
> 
> Correct me if I'm wrong, as I am not that familiar with the way that 
> integration of raw images works:
> 
> Could it be possible for a new/already existing software to store reflections 
> (area, intensity from center to border, position x/y on the image, and 
> information of the image) in a lightweight and text only file ? Possibly a 
> new format to be used for integration ?
> 
> While those text files would be heavy, they'd be still lighter than raw 
> images and the whole useless white space they carry with them between 
> reflections.
> 
> If not possible, could we imagine to eliminate all the unused space on these 
> ? Like a super raw image diet-plan for the incoming summer !
> 
> Best regards,
> 
> Julien CAPPELE
> Université de Lorraine, Nancy, France
> PhD student - 2nd Year
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Julien Cappèle]

Hi everyone,

There are some very interesting ideas. 

Though I agree with you Clement that raw images are amazing to work with as you 
can use any software you are confortable with, we cannot forget that depositing 
several TB of data for each lab would be bad for ecological reason. And because 
detectors are always improving (thank you all!), size of data will increase 
exponentially. 

Correct me if I'm wrong, as I am not that familiar with the way that 
integration of raw images works:

Could it be possible for a new/already existing software to store reflections 
(area, intensity from center to border, position x/y on the image, and 
information of the image) in a lightweight and text only file ? Possibly a new 
format to be used for integration ?

While those text files would be heavy, they'd be still lighter than raw images 
and the whole useless white space they carry with them between reflections.

If not possible, could we imagine to eliminate all the unused space on these ? 
Like a super raw image diet-plan for the incoming summer !

Best regards,

Julien CAPPELE
Université de Lorraine, Nancy, France
PhD student - 2nd Year



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Andreas Förster]

Hi Clemens,

this is curious.  You are right that there's a direct link to the raw data
on 6vs4, but there isn't one on http://www.rcsb.org/structure/6H56.  I'll
contact RCSB to see where the problem lies.

All best.


Andreas



On Thu, Mar 19, 2020 at 8:34 AM Clemens Vonrhein 
wrote:

> Hi Andreas,
>
> On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote:
> > - The link to the raw data can be found inside the mmCIF file under
> > _pdbx_related_exp_data_set.data_reference.  Whether it's also shown on
> one
> > of the PDB sites is up to the designers of these sides.  I cannot find a
> > link to the experimental data on rcsb.org.
>
> They are available near the bottom of a rcsb.org page ("Experimental
> Data & Validation" section) - see e.g. 6VS4 page
>
>   http://www.rcsb.org/structure/6VS4
>
> (the newest deposited PDB structure with deposited data recorded).
>
> Cheers
>
> Clemens
>
> PS: if anyone is in need of a simple script for finding and
> downloading such PDB entries, please let me know.
>
>



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Clemens Vonrhein]

Dear Petr,

On Thu, Mar 19, 2020 at 06:45:31AM +, Petr Kolenko wrote:
> For those of you who are in touch with these data, would deposition
> of unmerged intensities in P1 in the whole detector range instead of
> complete dataset be good enough to „correctly“ re-evaluete the
> structure? Or is there a doubt that even this approach would not
> lead to optimal structure?

It would be a step in the right direction, yes ... but:

 * It assumes that all spots have been integrated and nothing else
   than those spots: there can be cases of missed unit cell
   duplications or incorrect enforcement of a unit cell and symmetry
   (because those crystals always come in a known cell/SG, right?).

 * We'll still be stuck with a particular intergration program and a
   particular set of user decisions how to run it. Yes, all modern
   data processing programs and packages are usually doing a great job
   if run in (more or less) default mode on (more or less) good
   crystals. But not everything is lysozyme/thaumatin/XYZ collected
   fine-sliced on a PAD with low-dose, high-multiplicity on a well
   calibrated instrument ;-)

 * If integration was done in P1 the cell parameter restraints of the
   (potentiually different) true SG were not enforced - which can lead
   to incorrect cell parameters (which has knock-on effects in
   refinement ... remember the WhatIf check for correct cell
   parameter?).

   If integration was done in a non-P1 SG and that choice was
   incorrect: how do we know that those cell parameters didn't enforce
   an incorrect set of cell parameter restraints, leading to poor
   integration? Again: different programs have different ways of
   assigning pixels (and their counts) to a reflection intensity
   (concepts like shoebox, profile-fitting, pixel-labeling etc all
   come to mind).

 * Integration itself can be suboptimal if there are issues with the
   crystal (ice rings, split, multiple lattices etc), the instrument
   (damaged pixels, beam jitter, incorrect countrate cut-off handling
   etc) or the experiment (radiation damage etc). Data processing
   defaults might not always work correctly/best for all cases.

 * The raw images allow such corrections (damaged pixels not yet in
   pixel mask, incorrect handling of countrate_cutoff) and additional
   analysis (e.g. radiation damage analysis a la F(early)-F(late) maps
   [1]).

So the raw integrated (not scaled/corrected) and unmerged intensities
might indeed often be good enough, but if we are going to try and
deposit more than just the merged and scaled intensities/amplitudes
(as we do now) - and this will involve additional work and change from
our side - then why not bite the bullet once and try to go all the way
to raw images:

  * The infrastructure is already in place (proteindiffraction.org,
data.sbgrid.org, zenodo.org, wwPDB DOIs, etc), ready for use right
now.

  * From experience at multiple worshops: everyone is comfortable to
start data processing from raw images using the various software
tools out there that people are familiar with (while jumping in
half way is probably more challenging to non power-users).

Anyway, just some ideas - from someone downloading nearly all deposited
raw image data on a regular basis for testing and developing data
processing software (and finding a lot of issues in our software this
way ... as well as issues with experiments and sometimes the
instrument).

Cheers

Clemens

[1] as e.g. done in autoPROC+BUSTER



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Clemens Vonrhein]

Hi Andreas,

On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote:
> - The link to the raw data can be found inside the mmCIF file under
> _pdbx_related_exp_data_set.data_reference.  Whether it's also shown on one
> of the PDB sites is up to the designers of these sides.  I cannot find a
> link to the experimental data on rcsb.org.

They are available near the bottom of a rcsb.org page ("Experimental
Data & Validation" section) - see e.g. 6VS4 page

  http://www.rcsb.org/structure/6VS4

(the newest deposited PDB structure with deposited data recorded).

Cheers

Clemens

PS: if anyone is in need of a simple script for finding and
downloading such PDB entries, please let me know.



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Petr Kolenko]

For those of you who are in touch with these data, would deposition of unmerged 
intensities in P1 in the whole detector range instead of complete dataset be 
good enough to „correctly“ re-evaluete the structure? Or is there a doubt that 
even this approach would not lead to optimal structure?

My personal opinion is that storage of raw data is not a green way of science. 
I believe that in 50 years (not my bussines in these time), the storage and 
maintaining of the data we acquire in these times may take a whole capacity of 
one powerplant. Not talking about the material consumption. In some cases, 
re-doing of the complete thing may after all be less damaging the environment 
than storage of whole bunch of data that are irrelevant because of the perfect 
work that has been done previously and does not need re-evaluation. Is there a 
way to improve the (diffraction data vs. structure) validation tools?

I know, science cannot be a green technology. But some limitations should be 
considered, at least. Of course, I may be absolutely wrong.

A good question now could be, is there something else that the community could 
do for accelerating the research of SARS-CoV-2? May be, some people could offer 
their spare time to help the others with someting?

Best regards,
Petr

From: CCP4 bulletin board  On Behalf Of Andreas Förster
Sent: Thursday, March 19, 2020 7:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

As someone who's done this (for one structure of minor significance), I would 
like to make a few comments:

- I highly encourage deposition of raw data.  Why would you not?  Now that many 
labs are shut is the time to do it for all these datasets hiding somewhere on 
abandoned hard disk.  These disks will break.  One hopes Zenodo will not.

- The link to the raw data can be found inside the mmCIF file under 
_pdbx_related_exp_data_set.data_reference.  Whether it's also shown on one of 
the PDB sites is up to the designers of these sides.  I cannot find a link to 
the experimental data on rcsb.org<http://rcsb.org>.  PDBe, in contrast, has a 
clearly visible box linking to "Experimental raw data" on the start page of the 
structure.

Deposit your raw data!


Andreas



On Wed, Mar 18, 2020 at 11:31 PM Gerard Bricogne 
mailto:g...@globalphasing.com>> wrote:
Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as 
data.sbgrid.org<http://data.sbgrid.org>, zenodo.org<http://zenodo.org>,
proteindiffraction.org<http://proteindiffraction.org> or any other cloud-based 
data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.

Experts making use of those raw data would be encouraged to document, in as
much detail as possible, how particular programs or workflows could be used
on those structures/datasets to obtain the best results. This would be a
kind of "virtual workshop", a particularly valuable collective activity at
the present time when several in-person workshops (e.g. RapiData) have been
cancelled and many meetings are in limbo for several months.

The latter activity would benefit from having a centralised facility set up
for the experts to post their results and annotations: we could create such
a facility, but other, larger groups might want to consider doing so.


With best wishes,

Clemens & Gerard.



To unsubscribe

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Andreas Förster]

As someone who's done this (for one structure of minor significance), I
would like to make a few comments:

- I highly encourage deposition of raw data.  Why would you not?  Now that
many labs are shut is the time to do it for all these datasets hiding
somewhere on abandoned hard disk.  These disks will break.  One hopes
Zenodo will not.

- The link to the raw data can be found inside the mmCIF file under
_pdbx_related_exp_data_set.data_reference.  Whether it's also shown on one
of the PDB sites is up to the designers of these sides.  I cannot find a
link to the experimental data on rcsb.org.  PDBe, in contrast, has a
clearly visible box linking to "Experimental raw data" on the start page of
the structure.

Deposit your raw data!


Andreas



On Wed, Mar 18, 2020 at 11:31 PM Gerard Bricogne 
wrote:

> Dear colleagues,
>
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to improve these if refinements could be repeated after some reprocessing
> and further analysis of the raw diffraction images, rather than against the
> deposited merged data. This statement should in no way be construed as a
> criticism of the remarkable achievements of the research groups concerned,
> who have been operating under tremendous time pressure, but as an exciting
> opportunity to push methods to their limits on a uniquely significant class
> of structures.
>
> Another consideration is that the various logistical problems created by
> COVID-19 may soon make it increasingly difficult to collect new diffraction
> data on potential drug targets relevant to the fight against SARS-CoV-2,
> underlining the importance of ensuring that the best results be obtained
> from every dataset actually collected, and that the most useful conclusions
> be drawn from the analysis of those datasets towards improving the quality
> of subsequent data collections.
>
> On this basis we would like to propose that special efforts be made to
> grant
> public access to the raw image data associated with any SARS-CoV-2 related
> structure that is deposited into the PDB. This can be done by (1) archiving
> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> proteindiffraction.org or any other cloud-based data-sharing service, and
> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> could be extended to datasets that investigators would like to offer to
> interested methods developers or expert users at the pre-deposition stage.
>
> Experts making use of those raw data would be encouraged to document, in as
> much detail as possible, how particular programs or workflows could be used
> on those structures/datasets to obtain the best results. This would be a
> kind of "virtual workshop", a particularly valuable collective activity at
> the present time when several in-person workshops (e.g. RapiData) have been
> cancelled and many meetings are in limbo for several months.
>
> The latter activity would benefit from having a centralised facility set up
> for the experts to post their results and annotations: we could create such
> a facility, but other, larger groups might want to consider doing so.
>
>
> With best wishes,
>
> Clemens & Gerard.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Soisson, Stephen M]

A wonderful idea Gerard and Clemens.

Sent from my iPhone

> On Mar 18, 2020, at 6:31 PM, Gerard Bricogne  wrote:
> 
> EXTERNAL EMAIL – Use caution with any links or file attachments.
> 
> Dear colleagues,
> 
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to improve these if refinements could be repeated after some reprocessing
> and further analysis of the raw diffraction images, rather than against the
> deposited merged data. This statement should in no way be construed as a
> criticism of the remarkable achievements of the research groups concerned,
> who have been operating under tremendous time pressure, but as an exciting
> opportunity to push methods to their limits on a uniquely significant class
> of structures.
> 
> Another consideration is that the various logistical problems created by
> COVID-19 may soon make it increasingly difficult to collect new diffraction
> data on potential drug targets relevant to the fight against SARS-CoV-2,
> underlining the importance of ensuring that the best results be obtained
> from every dataset actually collected, and that the most useful conclusions
> be drawn from the analysis of those datasets towards improving the quality
> of subsequent data collections. 
> 
> On this basis we would like to propose that special efforts be made to grant
> public access to the raw image data associated with any SARS-CoV-2 related
> structure that is deposited into the PDB. This can be done by (1) archiving
> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> proteindiffraction.org or any other cloud-based data-sharing service, and
> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> could be extended to datasets that investigators would like to offer to
> interested methods developers or expert users at the pre-deposition stage.
> 
> Experts making use of those raw data would be encouraged to document, in as
> much detail as possible, how particular programs or workflows could be used
> on those structures/datasets to obtain the best results. This would be a
> kind of "virtual workshop", a particularly valuable collective activity at
> the present time when several in-person workshops (e.g. RapiData) have been
> cancelled and many meetings are in limbo for several months.
> 
> The latter activity would benefit from having a centralised facility set up
> for the experts to post their results and annotations: we could create such
> a facility, but other, larger groups might want to consider doing so. 
> 
> 
> With best wishes,
> 
> Clemens & Gerard.
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Notice:  This e-mail message, together with any attachments, contains
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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Diana Tomchick]

​Frankly this is a great idea for datasets on any projects. I've been so busy 
the last 3-4 years that I have been unable to do it for my projects, but now I 
should be able to get it done. Not to mention trying to solve a couple of those 
pesky structures that have proven tough nuts to crack.


Diana


**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, March 18, 2020 5:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

EXTERNAL MAIL

What a great idea? Have you approached the depositors? Eleanor

On Wed, 18 Mar 2020 at 22:31, Gerard Bricogne 
mailto:g...@globalphasing.com>> wrote:
Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as 
data.sbgrid.org<http://data.sbgrid.org>, zenodo.org<http://zenodo.org>,
proteindiffraction.org<http://proteindiffraction.org> or any other cloud-based 
data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.

Experts making use of those raw data would be encouraged to document, in as
much detail as possible, how particular programs or workflows could be used
on those structures/datasets to obtain the best results. This would be a
kind of "virtual workshop", a particularly valuable collective activity at
the present time when several in-person workshops (e.g. RapiData) have been
cancelled and many meetings are in limbo for several months.

The latter activity would benefit from having a centralised facility set up
for the experts to post their results and annotations: we could create such
a facility, but other, larger groups might want to consider doing so.


With best wishes,

Clemens & Gerard.



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CAUTION: This email originated from outside UTSW. Please be cautious of links 
or attachments, and validate the sender's email address before replying.



UT Southwestern


Medical Center



The future of medicine, today.




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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Eleanor Dodson]

What a great idea? Have you approached the depositors? Eleanor

On Wed, 18 Mar 2020 at 22:31, Gerard Bricogne 
wrote:

> Dear colleagues,
>
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to improve these if refinements could be repeated after some reprocessing
> and further analysis of the raw diffraction images, rather than against the
> deposited merged data. This statement should in no way be construed as a
> criticism of the remarkable achievements of the research groups concerned,
> who have been operating under tremendous time pressure, but as an exciting
> opportunity to push methods to their limits on a uniquely significant class
> of structures.
>
> Another consideration is that the various logistical problems created by
> COVID-19 may soon make it increasingly difficult to collect new diffraction
> data on potential drug targets relevant to the fight against SARS-CoV-2,
> underlining the importance of ensuring that the best results be obtained
> from every dataset actually collected, and that the most useful conclusions
> be drawn from the analysis of those datasets towards improving the quality
> of subsequent data collections.
>
> On this basis we would like to propose that special efforts be made to
> grant
> public access to the raw image data associated with any SARS-CoV-2 related
> structure that is deposited into the PDB. This can be done by (1) archiving
> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> proteindiffraction.org or any other cloud-based data-sharing service, and
> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> could be extended to datasets that investigators would like to offer to
> interested methods developers or expert users at the pre-deposition stage.
>
> Experts making use of those raw data would be encouraged to document, in as
> much detail as possible, how particular programs or workflows could be used
> on those structures/datasets to obtain the best results. This would be a
> kind of "virtual workshop", a particularly valuable collective activity at
> the present time when several in-person workshops (e.g. RapiData) have been
> cancelled and many meetings are in limbo for several months.
>
> The latter activity would benefit from having a centralised facility set up
> for the experts to post their results and annotations: we could create such
> a facility, but other, larger groups might want to consider doing so.
>
>
> With best wishes,
>
> Clemens & Gerard.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Gerard Bricogne]

Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections. 

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as data.sbgrid.org, zenodo.org,
proteindiffraction.org or any other cloud-based data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.

Experts making use of those raw data would be encouraged to document, in as
much detail as possible, how particular programs or workflows could be used
on those structures/datasets to obtain the best results. This would be a
kind of "virtual workshop", a particularly valuable collective activity at
the present time when several in-person workshops (e.g. RapiData) have been
cancelled and many meetings are in limbo for several months.

The latter activity would benefit from having a centralised facility set up
for the experts to post their results and annotations: we could create such
a facility, but other, larger groups might want to consider doing so. 


With best wishes,

Clemens & Gerard.



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Re: [ccp4bb] Powder diffraction database

[Irene Margiolaki]

Regarding X-ray Powder Diffraction software 

http://www.ccp14.ac.uk/ 

Regarding search match procedures and databases there are several 

https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ 

http://www.icdd.com/?gclid=EAIaIQobChMI1NGPpIOZ5gIVhkPTCh3E4gcyEAAYASAAEgIQhPD_BwE


http://www.ba.ic.cnr.it/softwareic/qualxweb/ 

https://www.researchgate.net/post/Are_there_any_freely_available_X-Ray_powder_diffraction_peak_identification_search-match_software_packages


http://cod.iutcaen.unicaen.fr/ 

https://www.malvernpanalytical.com/en/products/category/software/x-ray-diffraction-software/highscore-with-plus-option?creative=338894239672=highscore%20plus=e=g=c=EAIaIQobChMIkaLcnISZ5gIVFON3Ch1rvQQIEAAYASAAEgJIRfD_BwE


Regarding protein powder data, unfortunately there is still not a
database available. However, we can help in this matter via our inhouse
databases for anyone who is interested. More info is now available in
the latest volume H of the Int. Tables of Crystallography [1] and our
team's web site [2]. 

I hope this is helpful. 

all the best 

Irene Margiolaki 

Στις 2019-12-02 11:51, Peer Mittl έγραψε:

> Could someone please give me some advice on how to query a publicly available 
> powder diffraction database? Upon (protein) crystallization we always get 
> large spherulites of an inorganic compound and I would like to know what it 
> is. It should be possible to use the scattering angles of these spherulites 
> (its definitely not ice) to query a powder diffraction database. But which 
> database (e.g. CSD) and how?
> 
> All the best,
> Peer
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
Irene Margiolaki, PhD
Associate Professor, Department of Biology, Section of Genetics, Cell
Biology and Development, University of Patras, GR-26500, Patras, Greece
Office (Room Number 212) Tel: +302610997408, X-ray Lab (Room Number Y31)
Tel: +302610996773, Crystallization Lab (Room Number 226) Tel.:
+302610997200
Web sites:
http://www.biology.upatras.gr/index.php?option=com_content=article=652:2012-11-01-08-31-26=48=336
https://sites.google.com/view/margiolaki-biology-upat

 

Links:
--
[1]
https://drive.google.com/file/d/1KTnkln0EtWBR95YnxY1JyeDUJdZo7uuQ/view
[2] https://sites.google.com/view/margiolaki-biology-upat/home



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Re: [ccp4bb] Powder diffraction database

[Pierre Rizkallah]

The database you want is at the International centre for diffraction data, 
icdd.com , and look in the Powder Diffraction File, PDF . I have never used it 
myself, and I imagine you need to query it with a diffraction pattern, however 
it can be parsed. Taking a simile of a pattern extracted from diffraction 
images, intended for protein crystal diffraction, may not be simple, as there 
often is preferred orientation, which gives lumps of high intensity around the 
ring. But it might be sufficient for 'phase recognition'. CDS is intended for 
curated, refined, single crystal structures, an extremely useful resource, but 
not for what you have in  mind. Good Luck.

Pierre Rizkallah
***
Dr Pierre Rizkallah, Senior Lecturer Structural Biology 
Institute of Infection & Immunology, Sir Geraint Evans Building, 
School of Medicine, Heath Campus, Cardiff, CF14 4XN
email: rizkall...@cardiff.ac.uk        phone: +44 29 2074 2248
http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre

-Original Message-
From: CCP4 bulletin board  On Behalf Of Peer Mittl
Sent: 02 December 2019 09:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Powder diffraction database

Could someone please give me some advice on how to query a publicly available 
powder diffraction database? Upon (protein) crystallization we always get large 
spherulites of an inorganic compound and I would like to know what it is. It 
should be possible to use the scattering angles of these spherulites (its 
definitely not ice) to query a powder diffraction database. But which database 
(e.g. CSD) and how?

All the best,
Peer



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Re: [ccp4bb] Powder diffraction database

[Harry Powell]

From memory, I’d look at the ICSD first; I think it’s got lots of powder 
information.

From what I remember, CSD is entirely single crystal (though there might be 
some powder structures there), and is not what many people would call “publicly 
available”.

You may or may not have some luck looking at COD (the Crystallography Open 
Database, not the demersal or pelagic fish of the same name….)

How would you do it? Well, your googling skills are probably as good as mine, 
if not better.

Harry

> On 2 Dec 2019, at 09:51, Peer Mittl  wrote:
> 
> Could someone please give me some advice on how to query a publicly available 
> powder diffraction database? Upon (protein) crystallization we always get 
> large spherulites of an inorganic compound and I would like to know what it 
> is. It should be possible to use the scattering angles of these spherulites 
> (its definitely not ice) to query a powder diffraction database. But which 
> database (e.g. CSD) and how?
> 
> All the best,
> Peer
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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[ccp4bb] Powder diffraction database

[Peer Mittl]

Could someone please give me some advice on how to query a publicly 
available powder diffraction database? Upon (protein) crystallization we 
always get large spherulites of an inorganic compound and I would like 
to know what it is. It should be possible to use the scattering angles 
of these spherulites (its definitely not ice) to query a powder 
diffraction database. But which database (e.g. CSD) and how?


All the best,
Peer



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[ccp4bb] Workshop "Diffraction Data Collection Using Synchrotron Radiation"

[Manfred S. Weiss]

I would hereby like to announce the 6th edition of the workshop
"Diffraction Data Collection Using Synchrotron Radiation", which
will take place from July 04-06, 2019 at the BESSY II storage
ring of the Helmholtz-Zentrum Berlin for Materials and Energy
(HZB) in Berlin.

This workshop is the successor to five previous successful work-
shops, which took place in 2007, 2009, 2011, 2013 and 2016. It is
sponsored by the German Society for Crystallography (DGK) and
organised in cooperation with the DGK Working Group 1 (Biological
Structures).

The workshop comprises a series of basic lectures on the topic
and two extended practical sessions. It is aimed at PhD students
in Biological Crystallography with little or no experience in
diffraction data collection at a synchrotron. The practical sessions
will take place at the MX beamlines located at the electron storage
ring BESSY II.

The workshop fee is 100 EUR for DGK-members and 120 EUR for non-members.
This fee covers all conference material as well as board and lodging
for two nights on the campus in Berlin-Adlershof.

For more information please visit the web page
https://www.helmholtz-berlin.de/events/dgk/index_en.html

The application page is now open. Since the number of students will
have to be limited to 20 in order to ensure that the practical sessions
run efficiently, we expect that the workshop will fill up quickly.
Participants are also expected to present a poster on their own work.
As previously, the best poster will be awarded with an attractive prize.
##

Manfred Weiss

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



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Re: [ccp4bb] Weird diffraction pattern

[Sam Tang]

Dear all

Thanks for all the input both on- and off- the list. We shall definitely
look into these suggestions further and report again here in due course.

Kind regards

Sam


On Tue, 9 Oct 2018 at 19:12, Sam Tang  wrote:

> Dear all
>
> Hello. We recently shot a crystal (a protein with small molecule as
> ligand) at a synchrotron source and see a weird pattern. (
> https://drive.google.com/file/d/11bEtTJzKaAB5ZybezgN1cqBrckSRg2OV/view?usp=sharing
> )
>
> Crystal was grown in Citric acid and ammonium sulfate, cryoprotected with
> glycerol.
>
> At first we thought it was a protein crystal contaminated with salt but on
> second thought, the lowest resolution spot was at around 7 A, which doesn't
> make sense for a protein. So we would like to solicit your experience and
> perhaps someone may have encountered similar pattern before?
>
> Many thanks.
>
> Kind regards
>
> Sam
>
>



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] Weird diffraction pattern

[Herman . Schreuder]

To me, it looks like some intergrown salt crystal.
HS

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang
Gesendet: Dienstag, 9. Oktober 2018 13:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Weird diffraction pattern

Dear all

Hello. We recently shot a crystal (a protein with small molecule as ligand) at 
a synchrotron source and see a weird pattern. 
(https://drive.google.com/file/d/11bEtTJzKaAB5ZybezgN1cqBrckSRg2OV/view?usp=sharing<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_11bEtTJzKaAB5ZybezgN1cqBrckSRg2OV_view-3Fusp-3Dsharing=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=ExvzTpwCzYQcP3Idr9vHnPcGFh0UXDAKsEB7jClqsF0=4dUd1KLQYV5G8_jUYdS8kORXsEkS-0kwKqiGRj5dvDg=>)

Crystal was grown in Citric acid and ammonium sulfate, cryoprotected with 
glycerol.

At first we thought it was a protein crystal contaminated with salt but on 
second thought, the lowest resolution spot was at around 7 A, which doesn't 
make sense for a protein. So we would like to solicit your experience and 
perhaps someone may have encountered similar pattern before?

Many thanks.

Kind regards

Sam




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Weird diffraction pattern

[colin.n...@diamond.ac.uk]

Hello again
It could be a powder pattern aligned along one axis?
The cell I gave (actually orthorhombic) is one of the crystal forms of one of 
the components in your mixture – glycerol. You may have another form of 
glycerol. It is worth checking.

Colin
PS I think glycerol diffraction has been raised previously on CCP4bb


From: Sam Tang 
Sent: 09 October 2018 15:02
To: Nave, Colin (DLSLtd,RAL,LSCI) 
Cc: ccp4bb 
Subject: Re: [ccp4bb] Weird diffraction pattern

Hello Colin

Although the unit cell dimensions from mosflm should be largely unreliable in 
this case, the software actually returned a P2 space group with a=24.6, b=7.5, 
c=69.5  where b is so short that it resembles a small molecule crystal.

Regards

Sam
Sam

On Tue, 9 Oct 2018 at 20:53, 
colin.n...@diamond.ac.uk<mailto:colin.n...@diamond.ac.uk> 
mailto:colin.n...@diamond.ac.uk>> wrote:
Sam
Would this unit cell index some of the spots?
a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A.
  Colin

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Sam Tang
Sent: 09 October 2018 12:13
To: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: [ccp4bb] Weird diffraction pattern

Dear all

Hello. We recently shot a crystal (a protein with small molecule as ligand) at 
a synchrotron source and see a weird pattern. 
(https://drive.google.com/file/d/11bEtTJzKaAB5ZybezgN1cqBrckSRg2OV/view?usp=sharing)

Crystal was grown in Citric acid and ammonium sulfate, cryoprotected with 
glycerol.

At first we thought it was a protein crystal contaminated with salt but on 
second thought, the lowest resolution spot was at around 7 A, which doesn't 
make sense for a protein. So we would like to solicit your experience and 
perhaps someone may have encountered similar pattern before?

Many thanks.

Kind regards

Sam




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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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Re: [ccp4bb] Weird diffraction pattern

[Sam Tang]

Hello Colin

Although the unit cell dimensions from mosflm should be largely unreliable
in this case, the software actually returned a P2 space group with a=24.6,
b=7.5, c=69.5  where b is so short that it resembles a small molecule
crystal.

Regards

Sam
Sam


On Tue, 9 Oct 2018 at 20:53, colin.n...@diamond.ac.uk <
colin.n...@diamond.ac.uk> wrote:

> Sam
>
> Would this unit cell index some of the spots?
>
> a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A.
>
>   Colin
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Sam
> Tang
> *Sent:* 09 October 2018 12:13
> *To:* ccp4bb 
> *Subject:* [ccp4bb] Weird diffraction pattern
>
>
>
> Dear all
>
>
>
> Hello. We recently shot a crystal (a protein with small molecule as
> ligand) at a synchrotron source and see a weird pattern. (
> https://drive.google.com/file/d/11bEtTJzKaAB5ZybezgN1cqBrckSRg2OV/view?usp=sharing
> )
>
>
>
> Crystal was grown in Citric acid and ammonium sulfate, cryoprotected with
> glycerol.
>
>
>
> At first we thought it was a protein crystal contaminated with salt but on
> second thought, the lowest resolution spot was at around 7 A, which doesn't
> make sense for a protein. So we would like to solicit your experience and
> perhaps someone may have encountered similar pattern before?
>
>
>
> Many thanks.
>
>
>
> Kind regards
>
>
> Sam
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
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> Any opinions expressed within this e-mail are those of the individual and
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> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
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Re: [ccp4bb] Weird diffraction pattern

[colin.n...@diamond.ac.uk]

Sam
Would this unit cell index some of the spots?
a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A.
  Colin

From: CCP4 bulletin board  On Behalf Of Sam Tang
Sent: 09 October 2018 12:13
To: ccp4bb 
Subject: [ccp4bb] Weird diffraction pattern

Dear all

Hello. We recently shot a crystal (a protein with small molecule as ligand) at 
a synchrotron source and see a weird pattern. 
(https://drive.google.com/file/d/11bEtTJzKaAB5ZybezgN1cqBrckSRg2OV/view?usp=sharing)

Crystal was grown in Citric acid and ammonium sulfate, cryoprotected with 
glycerol.

At first we thought it was a protein crystal contaminated with salt but on 
second thought, the lowest resolution spot was at around 7 A, which doesn't 
make sense for a protein. So we would like to solicit your experience and 
perhaps someone may have encountered similar pattern before?

Many thanks.

Kind regards

Sam




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

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This e-mail and any attachments may contain confidential, copyright and or 
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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
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Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

[Philippe BENAS]

Dear Joseph,
I fully agree with Daniel Himmel's answer but you might be able to "index" your 
reflections and get a approximate cell parameters.
I did that in the past with crystals that diffracted very poorly up to 15 
angst. I used HKL200 at that time, cheated with the distance (HKL2000 won't 
accept indexing with too low resolution spots) and selected individual spots 
manually.It was enough for making Matthews analysis for each putative space 
group.The complex formation between the protein and the RNA was confirmed by a 
stoechiometric amount of each macromolecule resulting from OD spectra 
deconvolution taken on dissolved crystals, using a spectrum for the protein 
alone and a spectrum for the RNA alone as references.
Best regards,
Philippe Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Joseph Ho <sbddintai...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Lundi 12 mars 2018 12h54
 Objet : [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone 
crystal?
   
Dear all:


I would like to seek your wisdom on our latest diffraction pattern. We
have been working on protein/DNA complex. The protein and DNA have
similar MW. By binding assay, we know the minimal length of DNA. (The
Kd is 0.1-1 microMolar and we can see the complex formation in size
exclusion chromatography up to 200mM NaCl but also some unbound form)
After trying different length of DNA, we recently obtained many
crystal hits (the percipient is either PEG400 or MPD). The final ratio
(prior to protein crystallization) between protein and DNA is 1:1.6
considering some loss of protein during concentration. The crystal is
birefringent. Since high conc. of PEG400 (MPD), the crystals were
directly frozen in liquid N2. However, crystals only diffract to 8-10
angstrom (anisotropic) and also  weird striking line are present
(please see attachment). Do you think if it is  DNA alone crystal or
protein/DNA complex crystal?
How should I improve the diffraction quality?



PS. We have done some tests. For example, set up the same conditions
with DNA alone. I also tried to dissolve crystals in Bradford assay
solution and I believe I saw some blueish color. But none of these
tests are conclusive.

Thanks for your suggestion.

Joseph


   

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

[Daniel M. Himmel, Ph. D.]

The diffraction patterns clearly show an overlap of two or more

lattices, which either means you didn’t have a single crystal at the

start or it was damaged during the flash-cooling process.  PEG 400

is generally a good cryoprotectant at ≥20%, but I would recommend using

at least 25% to be certain no ice formation damages the crystal lattice.


The high mosaicity makes interpretation of the diffraction pattern open to

debate.  Some of the reflections look like they could originate from
protein,

since they indicate long distance repeats.  Some double-spots suggest a
cracked

crystal with high mosaicity.  It’s a difficult call for me, but I think the
layer

lines look roughly like an hour glass shape, which is characteristically

seen in DNA patterns and arises from the double-helical structure.

Again, the layer lines suggest at least 2 or 3 lattices.  To pin down

whether you’re really looking at double-helical DNA, you need to

measure the real space distance suggested from layer lines (measure

the equiv. resolution from the reciprocal space origin).  I don’t have

time to look it up now, but there should be tell-tale layer line repeats

(if I recall correctly) at about 10 A and 34 A.  You can look for some

old papers by Francis Crick on helical theory (sorry I don’t have

the reference at my fingertips).  In summary, I would cautiously

surmise that you have a protein (small round spot reflections), bound

by DNA that is much more mobile (highly mosaic layer lines), and that

both the protein and DNA exist in multiple (probably three) lattices, but,

again, the distance repeats of the layer lines have to be measured to

see if they are consistent with double-helical DNA.


Try to get crystals that diffract better for more clarity.  Flash cool in

25% PEG 400 (or try combination of PEG 400 and PEG 200), or

vary the MPD concentration.  Good luck.


I hope this helps.


-Daniel



[image:
RnNZfQn2o2xpggJQqefCOervMbPIci5mujDPJnvl43kv6Rtxjyh5gHN_JKVzeU-aaGz3pePFgxfoAAtZJZNx8mveVTc-11j98EfuAJVcumUenA=s0-d-e1-ft.gif]Daniel
M. Himmel, Ph. D.

URL:  http://www.DanielMHimmel.com 


On Mon, Mar 12, 2018 at 11:24 AM, Joseph Ho  wrote:

> Dear Xiao and Hans:
>
> Thanks for your reply. We tried to index it but failed.
>
> Joseph
> On Mon, Mar 12, 2018 at 11:15 PM, Xiao Lei  wrote:
> > did you try to index it?  the cell dimensions may give you hint.
> >
> > On Mon, Mar 12, 2018 at 4:40 AM, Joseph Ho 
> wrote:
> >>
> >> Dear all:
> >>
> >>
> >> I would like to seek your wisdom on our latest diffraction pattern. We
> >> have been working on protein/DNA complex. The protein and DNA have
> >> similar MW. By binding assay, we know the minimal length of DNA. (The
> >> Kd is 0.1-1 microMolar and we can see the complex formation in size
> >> exclusion chromatography up to 200mM NaCl but also some unbound form)
> >> After trying different length of DNA, we recently obtained many
> >> crystal hits (the percipient is either PEG400 or MPD). The final ratio
> >> (prior to protein crystallization) between protein and DNA is 1:1.6
> >> considering some loss of protein during concentration. The crystal is
> >> birefringent. Since high conc. of PEG400 (MPD), the crystals were
> >> directly frozen in liquid N2. However, crystals only diffract to 8-10
> >> angstrom (anisotropic) and also  weird striking line are present
> >> (please see attachment). Do you think if it is  DNA alone crystal or
> >> protein/DNA complex crystal?
> >> How should I improve the diffraction quality?
> >>
> >>
> >>
> >> PS. We have done some tests. For example, set up the same conditions
> >> with DNA alone. I also tried to dissolve crystals in Bradford assay
> >> solution and I believe I saw some blueish color. But none of these
> >> tests are conclusive.
> >>
> >> Thanks for your suggestion.
> >>
> >> Joseph
> >
> >
>

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

[Joseph Ho]

Dear Xiao and Hans:

Thanks for your reply. We tried to index it but failed.

Joseph
On Mon, Mar 12, 2018 at 11:15 PM, Xiao Lei  wrote:
> did you try to index it?  the cell dimensions may give you hint.
>
> On Mon, Mar 12, 2018 at 4:40 AM, Joseph Ho  wrote:
>>
>> Dear all:
>>
>>
>> I would like to seek your wisdom on our latest diffraction pattern. We
>> have been working on protein/DNA complex. The protein and DNA have
>> similar MW. By binding assay, we know the minimal length of DNA. (The
>> Kd is 0.1-1 microMolar and we can see the complex formation in size
>> exclusion chromatography up to 200mM NaCl but also some unbound form)
>> After trying different length of DNA, we recently obtained many
>> crystal hits (the percipient is either PEG400 or MPD). The final ratio
>> (prior to protein crystallization) between protein and DNA is 1:1.6
>> considering some loss of protein during concentration. The crystal is
>> birefringent. Since high conc. of PEG400 (MPD), the crystals were
>> directly frozen in liquid N2. However, crystals only diffract to 8-10
>> angstrom (anisotropic) and also  weird striking line are present
>> (please see attachment). Do you think if it is  DNA alone crystal or
>> protein/DNA complex crystal?
>> How should I improve the diffraction quality?
>>
>>
>>
>> PS. We have done some tests. For example, set up the same conditions
>> with DNA alone. I also tried to dissolve crystals in Bradford assay
>> solution and I believe I saw some blueish color. But none of these
>> tests are conclusive.
>>
>> Thanks for your suggestion.
>>
>> Joseph
>
>

Re: [ccp4bb] weird diffraction pattern

[James Holton]

Hello Tang,

1) For MR, you might want to try a range of homologs, or even a stack of 
overlapping homologs. A normal modes server like elNemo might also help 
if it can predict the "bend" your molecule undergoes upon binding.  A 
long shot perhaps, but stranger things have happened.  You also might be 
able to find the DNA by molecular replacement.


2) radiation damage increases with photons/area, not time.  So no matter 
what your degrees/image you want the total shuttter-open time at the end 
of the data set to be below the damage limit of interest.  A little web 
app I made once might help: http://bl831.als.lbl.gov/xtallife.html .  
These days, there is no reason not to know how long your crystal will 
last before you push "collect", and it is definitely worth knowing.


-James Holton
MAD Scientist

On 7/28/2017 12:21 AM, Tang Chenjun wrote:

Hi,

Thanks to all who gave me suggestions concerning the weird diffraction pattern 
and I really appreciate it that Kay Diederichs help me processing my data set 
and answer my questions. Although the data set can be processed using HKL3000, 
XDS without problems, the Rwork/Rfree values are still above 0.5 after 
molecular replacement. There can be several reasons.
1) The structure change a lot after binding DNA, so it is not possible to find 
a solution using molecular replacement.
2) Strong radiation damage and 1.0 degree image widths prevent good integration 
results. It may be better to use 0.1 degree image widths.
3) Streaky spots appearing in certain directions because of anisotropy or 
lattice translocation disorder, or one very large unit cell dimension lying 
along the X-ray beam may also have an affect on data processing.

Now I am optimizing the crystals to address these problems.

Best wishes and thanks again for your help,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Sanishvili, Ruslan]

Hi Chenjun Tang,


I have not followed the original discussion, so my apologies if I am repeating 
the device already given to you.

Crystallization optimization is always a good idea - nothing beats good quality 
crystals. In addition,

you should try collecting few images, especially in the "bad" orientation of 
the crystal, at ambient temperature, from the samples that have NOT been 
cryo-protected yet.

You need to figure out if the cryo-protection and/or cryo-cooling are damaging 
your crystals.

Best,

Nukri


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

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




From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tang Chenjun 
<0910010...@cau.edu.cn>
Sent: Friday, July 28, 2017 2:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] weird diffraction pattern

Hi,

Thanks to all who gave me suggestions concerning the weird diffraction pattern 
and I really appreciate it that Kay Diederichs help me processing my data set 
and answer my questions. Although the data set can be processed using HKL3000, 
XDS without problems, the Rwork/Rfree values are still above 0.5 after 
molecular replacement. There can be several reasons.
1) The structure change a lot after binding DNA, so it is not possible to find 
a solution using molecular replacement.
2) Strong radiation damage and 1.0 degree image widths prevent good integration 
results. It may be better to use 0.1 degree image widths.
3) Streaky spots appearing in certain directions because of anisotropy or 
lattice translocation disorder, or one very large unit cell dimension lying 
along the X-ray beam may also have an affect on data processing.

Now I am optimizing the crystals to address these problems.

Best wishes and thanks again for your help,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Tang Chenjun]

Hi,

Thanks to all who gave me suggestions concerning the weird diffraction pattern 
and I really appreciate it that Kay Diederichs help me processing my data set 
and answer my questions. Although the data set can be processed using HKL3000, 
XDS without problems, the Rwork/Rfree values are still above 0.5 after 
molecular replacement. There can be several reasons.
1) The structure change a lot after binding DNA, so it is not possible to find 
a solution using molecular replacement.
2) Strong radiation damage and 1.0 degree image widths prevent good integration 
results. It may be better to use 0.1 degree image widths.
3) Streaky spots appearing in certain directions because of anisotropy or 
lattice translocation disorder, or one very large unit cell dimension lying 
along the X-ray beam may also have an affect on data processing.

Now I am optimizing the crystals to address these problems. 

Best wishes and thanks again for your help,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Gerard Bricogne]

Dear Gerd,

 I wasn't really giving much attention to the poke between the
ribs ;-) - for me the more serious matter was to see the merits of
pixel detectors over CCDs made light of, as if they didn't really make
much difference.

 If some people get carried away in the way you describe, well, it
doesn't hurt anyone; but if other people have very small, weakly
diffracting crystals and they are told that they will do as well on a
beamline with a CCD as on one with a Pilatus or an Eiger, then that
will hurt someone.

 The original topic was whether certain images presented without
any information about their angular width and recorded on a CCD were
sufficient to diagnose a diffraction quality problem. As they showed
evidene of at least one long axis, distinguishing streakiness from
plain angular overlap caused by too great an image width seemed the
most natural first step.

 The resolution I was talking about was resolving spots within
images and neighbouring images, either thanks to a detector with a
small PSF or thanks to a very fine image width. CCD detectors are poor
in the first option because of their extended PSF, so emphasis has
always been put on the importance of using the second one when pushed.
Pixel array detectors allow both options to be used simultaneously,
which is especially valuable in the investigation of crystals like
Tang's. Hence, again, my advice in the strict context of the initial
thread. 


 With best wishes,
 
  Gerard.

--
On Thu, Jul 13, 2017 at 02:39:58PM -0500, Gerd Rosenbaum wrote:
> Dear Gerard,
> 
>my "sound like a sales person" was meant as poking a little fun - nothing
> serious, of course.
> 
> I and our users like our not-so-new-anymore Pilatus3 6M. It's a great
> detector in many ways. But, there is a lot of hype that this detector solves
> all-problem, for instance fine slicing that is claimed to be only possible
> with a pixel array detector. People get carried away and use 0.01 degree
> slices even as the mosaicity of their sample is, say, 0.3 degree. Slicing
> beyond 1/3 of the mosaicity will gain you very little - only more frames,
> more processing time.
> 
> This discourse is already drifting away from the original topic of the
> thread so I will comment on the other arguments  you made like resolution in
> a private e-mail.
> 
> Best regards,
> 
> Gerd
> 
> On 13.07.2017 14:00, Gerard Bricogne wrote:
> >Dear Gerd,
> >
> >  I can assure you that I have no shares in Dectris nor any
> >commecial connections with them. What I do have is a lot of still
> >vivid memories of CCD images, with their wooly point-spread function
> >that was affected by fine-grained spatial variability as well as by
> >irredicible inaccuracies in the geometric corrections required to try
> >and undo the distortions introduced by the fiber-optic taper. By
> >comparison the pixel-array detectors have a very regular structure, so
> >that slight deviations from exact registering of the modules can be
> >calibrated with high accuracy, making it possible to get very small
> >residuals between calculated and observed spot positions. That, I
> >certainly never saw with CCD images.
> >
> >  I do think that asking for the image width was a highly pertinent
> >question in this case, that had not been asked. As a specialist you
> >might know how to use a CCD to good effect in fine-slicing mode, but
> >it is amazing how many people there are still out there who are told
> >to use 0.5 or even 1.0 degree image widths.
> >
> >  Compensating the poor PSF of a CCD by fine slicing in the angular
> >dimension is a tall order. With a Pilatus at 350mm from the crystal,
> >the angular separation between 174-micron pixels is 0.5 milliradian.
> >To achieve that separation in the angular (rotation) dimension, the
> >equivalent image width would have to be 0.03 degree. For an EIGER the
> >numbers become 75 microns, hence 0.21 milliradian i.e. 0.012 degree.
> >
> >  Hence my advice, untainted by any commercial agenda :-) .
> >  With best wishes,
> >   Gerard.
> >
> >--
> >On Thu, Jul 13, 2017 at 01:25:08PM -0500, Gerd Rosenbaum wrote:
> >>Dear Gerard,
> >>
> >>you sound like a sales person for Dectris. Fine slicing is perfectly fine
> >>with CCD detectors - it takes a bit longer because of the step scan instead
> >>of continuous scan. The read noise issue is often overstated compared to the
> >>sample induced scatter background. If for fine slicing at 0.05 degree or
> >>less the diffraction peaks go too close to the read noise make a longer
> >>exposure - signal goes up, ratio signal to sample-induced-BG less, as for
> >>any fine slicing, same read noise.
> >>
> >>It would be helpful to analyze the dense spot packing along layer lines if
> >>we knew the wavelength and the sample-to-detector distance (assuming this is
> >>a 300 mm detector) and the rotation width - as you pointed out. That would
> >>help to distinguish between multiple crystals (my 

Re: [ccp4bb] weird diffraction pattern

[Gerd Rosenbaum]

Dear Gerard,

   my "sound like a sales person" was meant as poking a little fun - 
nothing serious, of course.


I and our users like our not-so-new-anymore Pilatus3 6M. It's a great 
detector in many ways. But, there is a lot of hype that this detector 
solves all-problem, for instance fine slicing that is claimed to be only 
possible with a pixel array detector. People get carried away and use 
0.01 degree slices even as the mosaicity of their sample is, say, 0.3 
degree. Slicing beyond 1/3 of the mosaicity will gain you very little - 
only more frames, more processing time.


This discourse is already drifting away from the original topic of the 
thread so I will comment on the other arguments  you made like 
resolution in a private e-mail.


Best regards,

Gerd

On 13.07.2017 14:00, Gerard Bricogne wrote:

Dear Gerd,

  I can assure you that I have no shares in Dectris nor any
commecial connections with them. What I do have is a lot of still
vivid memories of CCD images, with their wooly point-spread function
that was affected by fine-grained spatial variability as well as by
irredicible inaccuracies in the geometric corrections required to try
and undo the distortions introduced by the fiber-optic taper. By
comparison the pixel-array detectors have a very regular structure, so
that slight deviations from exact registering of the modules can be
calibrated with high accuracy, making it possible to get very small
residuals between calculated and observed spot positions. That, I
certainly never saw with CCD images.

  I do think that asking for the image width was a highly pertinent
question in this case, that had not been asked. As a specialist you
might know how to use a CCD to good effect in fine-slicing mode, but
it is amazing how many people there are still out there who are told
to use 0.5 or even 1.0 degree image widths.

  Compensating the poor PSF of a CCD by fine slicing in the angular
dimension is a tall order. With a Pilatus at 350mm from the crystal,
the angular separation between 174-micron pixels is 0.5 milliradian.
To achieve that separation in the angular (rotation) dimension, the
equivalent image width would have to be 0.03 degree. For an EIGER the
numbers become 75 microns, hence 0.21 milliradian i.e. 0.012 degree.

  Hence my advice, untainted by any commercial agenda :-) .
  
  
  With best wishes,
  
   Gerard.


--
On Thu, Jul 13, 2017 at 01:25:08PM -0500, Gerd Rosenbaum wrote:

Dear Gerard,

you sound like a sales person for Dectris. Fine slicing is perfectly fine
with CCD detectors - it takes a bit longer because of the step scan instead
of continuous scan. The read noise issue is often overstated compared to the
sample induced scatter background. If for fine slicing at 0.05 degree or
less the diffraction peaks go too close to the read noise make a longer
exposure - signal goes up, ratio signal to sample-induced-BG less, as for
any fine slicing, same read noise.

It would be helpful to analyze the dense spot packing along layer lines if
we knew the wavelength and the sample-to-detector distance (assuming this is
a 300 mm detector) and the rotation width - as you pointed out. That would
help to distinguish between multiple crystals (my guess) and lattice
translocation disorder. Fine slicing is definitely needed to figure out what
the diffraction pattern at 120 degree could tell you in terms of strong
anisotropy .

Best regard.

Gerd

On 13.07.2017 08:20, Gerard Bricogne wrote:

Dear Tang,

  I noticed that your diffraction images seem to have been recorded
on a 3x3 CCD detector. With this type of detector, fine slicing is
often discouraged (because of the readout noise), and yet with the two
long cell axes you have, any form of thick (or only semi-fine) slicing
would result in spot overlaps.

  What, then, was your image width? Would you have access to a
beamline with a Pilatus detector so that you could collect fine-sliced
data?

  I would tend to agree with Herman that your crystals might be
cursed with lattice translocation disorder (LTD), but you might as
well try and put every chance of surviving this on your side by making
sure that you collect fine-sliced data. LTD plus thick slicing would
give you random data along the streaky direction. Use an image width
of at most 0.1 degree (0.05 would be better) on a Pilatus, and use XDS
to process your images.


  Good luck!
Gerard

--
On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun wrote:

Hi David,
Thanks for your comments. Although the spots become streaky in certain 
directions, I have processed the data in HKL3000 and imosflm, which suggested 
the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), 
completeness(94.8%), redundancy(4.6) are OK. When I tried to run Balbes with 
the solved native structure, the molecular replacement solution was poor. So I 
ran Balbes with the split domains of the native structure. Although the 
solutions were also 

Re: [ccp4bb] weird diffraction pattern

[Edward A. Berry]

Thanks for spelling it out!
Would that advice still hold if the mosaicity of the crystal is 0.7 degrees?
(I know, I should go read the paper., but . . .)
eab

On 07/13/2017 03:00 PM, Gerard Bricogne wrote:

Dear Gerd,

  I can assure you that I have no shares in Dectris nor any
commecial connections with them. What I do have is a lot of still
vivid memories of CCD images, with their wooly point-spread function
that was affected by fine-grained spatial variability as well as by
irredicible inaccuracies in the geometric corrections required to try
and undo the distortions introduced by the fiber-optic taper. By
comparison the pixel-array detectors have a very regular structure, so
that slight deviations from exact registering of the modules can be
calibrated with high accuracy, making it possible to get very small
residuals between calculated and observed spot positions. That, I
certainly never saw with CCD images.

  I do think that asking for the image width was a highly pertinent
question in this case, that had not been asked. As a specialist you
might know how to use a CCD to good effect in fine-slicing mode, but
it is amazing how many people there are still out there who are told
to use 0.5 or even 1.0 degree image widths.

  Compensating the poor PSF of a CCD by fine slicing in the angular
dimension is a tall order. With a Pilatus at 350mm from the crystal,
the angular separation between 174-micron pixels is 0.5 milliradian.
To achieve that separation in the angular (rotation) dimension, the
equivalent image width would have to be 0.03 degree. For an EIGER the
numbers become 75 microns, hence 0.21 milliradian i.e. 0.012 degree.

  Hence my advice, untainted by any commercial agenda :-) .


  With best wishes,

   Gerard.

--
On Thu, Jul 13, 2017 at 01:25:08PM -0500, Gerd Rosenbaum wrote:

Dear Gerard,

you sound like a sales person for Dectris. Fine slicing is perfectly fine
with CCD detectors - it takes a bit longer because of the step scan instead
of continuous scan. The read noise issue is often overstated compared to the
sample induced scatter background. If for fine slicing at 0.05 degree or
less the diffraction peaks go too close to the read noise make a longer
exposure - signal goes up, ratio signal to sample-induced-BG less, as for
any fine slicing, same read noise.

It would be helpful to analyze the dense spot packing along layer lines if
we knew the wavelength and the sample-to-detector distance (assuming this is
a 300 mm detector) and the rotation width - as you pointed out. That would
help to distinguish between multiple crystals (my guess) and lattice
translocation disorder. Fine slicing is definitely needed to figure out what
the diffraction pattern at 120 degree could tell you in terms of strong
anisotropy .

Best regard.

Gerd

On 13.07.2017 08:20, Gerard Bricogne wrote:

Dear Tang,

  I noticed that your diffraction images seem to have been recorded
on a 3x3 CCD detector. With this type of detector, fine slicing is
often discouraged (because of the readout noise), and yet with the two
long cell axes you have, any form of thick (or only semi-fine) slicing
would result in spot overlaps.

  What, then, was your image width? Would you have access to a
beamline with a Pilatus detector so that you could collect fine-sliced
data?

  I would tend to agree with Herman that your crystals might be
cursed with lattice translocation disorder (LTD), but you might as
well try and put every chance of surviving this on your side by making
sure that you collect fine-sliced data. LTD plus thick slicing would
give you random data along the streaky direction. Use an image width
of at most 0.1 degree (0.05 would be better) on a Pilatus, and use XDS
to process your images.


  Good luck!
Gerard

--
On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun wrote:

Hi David,
Thanks for your comments. Although the spots become streaky in certain 
directions, I have processed the data in HKL3000 and imosflm, which suggested 
the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), 
completeness(94.8%), redundancy(4.6) are OK. When I tried to run Balbes with 
the solved native structure, the molecular replacement solution was poor. So I 
ran Balbes with the split domains of the native structure. Although the 
solutions were also poor, I found the MR score of one solution above 35. On the 
basis of this solution, I tried to run Buccaneer and the Rfree could be 0.46. 
Unfortunately, there are four molecules in the asymmetric unit and it is to 
hard for me to reduce the Rfree further.

All best,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Gerard Bricogne]

Dear Gerd,

 I can assure you that I have no shares in Dectris nor any
commecial connections with them. What I do have is a lot of still
vivid memories of CCD images, with their wooly point-spread function
that was affected by fine-grained spatial variability as well as by 
irredicible inaccuracies in the geometric corrections required to try
and undo the distortions introduced by the fiber-optic taper. By
comparison the pixel-array detectors have a very regular structure, so
that slight deviations from exact registering of the modules can be
calibrated with high accuracy, making it possible to get very small
residuals between calculated and observed spot positions. That, I
certainly never saw with CCD images.

 I do think that asking for the image width was a highly pertinent
question in this case, that had not been asked. As a specialist you
might know how to use a CCD to good effect in fine-slicing mode, but
it is amazing how many people there are still out there who are told
to use 0.5 or even 1.0 degree image widths.

 Compensating the poor PSF of a CCD by fine slicing in the angular
dimension is a tall order. With a Pilatus at 350mm from the crystal,
the angular separation between 174-micron pixels is 0.5 milliradian.
To achieve that separation in the angular (rotation) dimension, the
equivalent image width would have to be 0.03 degree. For an EIGER the
numbers become 75 microns, hence 0.21 milliradian i.e. 0.012 degree.

 Hence my advice, untainted by any commercial agenda :-) .
 
 
 With best wishes,
 
  Gerard.

--
On Thu, Jul 13, 2017 at 01:25:08PM -0500, Gerd Rosenbaum wrote:
> Dear Gerard,
> 
> you sound like a sales person for Dectris. Fine slicing is perfectly fine
> with CCD detectors - it takes a bit longer because of the step scan instead
> of continuous scan. The read noise issue is often overstated compared to the
> sample induced scatter background. If for fine slicing at 0.05 degree or
> less the diffraction peaks go too close to the read noise make a longer
> exposure - signal goes up, ratio signal to sample-induced-BG less, as for
> any fine slicing, same read noise.
> 
> It would be helpful to analyze the dense spot packing along layer lines if
> we knew the wavelength and the sample-to-detector distance (assuming this is
> a 300 mm detector) and the rotation width - as you pointed out. That would
> help to distinguish between multiple crystals (my guess) and lattice
> translocation disorder. Fine slicing is definitely needed to figure out what
> the diffraction pattern at 120 degree could tell you in terms of strong
> anisotropy .
> 
> Best regard.
> 
> Gerd
> 
> On 13.07.2017 08:20, Gerard Bricogne wrote:
> >Dear Tang,
> >
> >  I noticed that your diffraction images seem to have been recorded
> >on a 3x3 CCD detector. With this type of detector, fine slicing is
> >often discouraged (because of the readout noise), and yet with the two
> >long cell axes you have, any form of thick (or only semi-fine) slicing
> >would result in spot overlaps.
> >
> >  What, then, was your image width? Would you have access to a
> >beamline with a Pilatus detector so that you could collect fine-sliced
> >data?
> >
> >  I would tend to agree with Herman that your crystals might be
> >cursed with lattice translocation disorder (LTD), but you might as
> >well try and put every chance of surviving this on your side by making
> >sure that you collect fine-sliced data. LTD plus thick slicing would
> >give you random data along the streaky direction. Use an image width
> >of at most 0.1 degree (0.05 would be better) on a Pilatus, and use XDS
> >to process your images.
> >
> >
> >  Good luck!
> >Gerard
> >
> >--
> >On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun wrote:
> >>Hi David,
> >>Thanks for your comments. Although the spots become streaky in certain 
> >>directions, I have processed the data in HKL3000 and imosflm, which 
> >>suggested the C2221 space group (66.59, 246.95 and 210.17). The 
> >>Rmerge(0.14), completeness(94.8%), redundancy(4.6) are OK. When I tried to 
> >>run Balbes with the solved native structure, the molecular replacement 
> >>solution was poor. So I ran Balbes with the split domains of the native 
> >>structure. Although the solutions were also poor, I found the MR score of 
> >>one solution above 35. On the basis of this solution, I tried to run 
> >>Buccaneer and the Rfree could be 0.46. Unfortunately, there are four 
> >>molecules in the asymmetric unit and it is to hard for me to reduce the 
> >>Rfree further.
> >>
> >>All best,
> >>
> >>Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Gerd Rosenbaum]

Dear Gerard,

you sound like a sales person for Dectris. Fine slicing is perfectly 
fine with CCD detectors - it takes a bit longer because of the step scan 
instead of continuous scan. The read noise issue is often overstated 
compared to the sample induced scatter background. If for fine slicing 
at 0.05 degree or less the diffraction peaks go too close to the read 
noise make a longer exposure - signal goes up, ratio signal to 
sample-induced-BG less, as for any fine slicing, same read noise.


It would be helpful to analyze the dense spot packing along layer lines 
if we knew the wavelength and the sample-to-detector distance (assuming 
this is a 300 mm detector) and the rotation width - as you pointed out. 
That would help to distinguish between multiple crystals (my guess) and 
lattice translocation disorder. Fine slicing is definitely needed to 
figure out what the diffraction pattern at 120 degree could tell you in 
terms of strong anisotropy .


Best regard.

Gerd

On 13.07.2017 08:20, Gerard Bricogne wrote:

Dear Tang,

  I noticed that your diffraction images seem to have been recorded
on a 3x3 CCD detector. With this type of detector, fine slicing is
often discouraged (because of the readout noise), and yet with the two
long cell axes you have, any form of thick (or only semi-fine) slicing
would result in spot overlaps.

  What, then, was your image width? Would you have access to a
beamline with a Pilatus detector so that you could collect fine-sliced
data?

  I would tend to agree with Herman that your crystals might be
cursed with lattice translocation disorder (LTD), but you might as
well try and put every chance of surviving this on your side by making
sure that you collect fine-sliced data. LTD plus thick slicing would
give you random data along the streaky direction. Use an image width
of at most 0.1 degree (0.05 would be better) on a Pilatus, and use XDS
to process your images.


  Good luck!
  
Gerard


--
On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun wrote:

Hi David,
Thanks for your comments. Although the spots become streaky in certain 
directions, I have processed the data in HKL3000 and imosflm, which suggested 
the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), 
completeness(94.8%), redundancy(4.6) are OK. When I tried to run Balbes with 
the solved native structure, the molecular replacement solution was poor. So I 
ran Balbes with the split domains of the native structure. Although the 
solutions were also poor, I found the MR score of one solution above 35. On the 
basis of this solution, I tried to run Buccaneer and the Rfree could be 0.46. 
Unfortunately, there are four molecules in the asymmetric unit and it is to 
hard for me to reduce the Rfree further.

All best,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Rajesh Kumar]

Hi Chenjun,

Few suggestions from my side. Process the data with XDS and look into
acentric intensity distribution (it indicates any twinning possibility).
Run XTRIAGE and SFCHECK to understand any twinning or pseudo translation
possibilities. Twinning can confuse the program and suggest you smaller
unit cell with higher symmetry. Your images indicate longer cell axis.
If you need more help, please send me an email.

Thank you
Rajesh

 ---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel: 718.430.2777  |  Fax: 718.430.8565




On Thu, Jul 13, 2017 at 3:56 AM, 唐晨骏 <0910010...@cau.edu.cn> wrote:

> hello everyone,
> I would like to seek your opinion on my crystal hits. I am working on a
> helicase
>
> of which the native structure is solved and the all solution statistics are
>
> fine. I am trying to crystallize and solve the structure of the
> protein/ssDNA
>
> complex. I recently got some hits from commercial screens using sitting
> drop
>
> vapor diffusion. After crystallization optimization, these crystals
> diffract
>
> weakly but to 3.2 Angstroms for the longer exposure time. However, when the
>
> crystals rotate between 120 degrees to 180 degrees, the spots become
> streaky
>
> (attached), no matter the crystals are hexagonal or flaky. I have tried to
>
> determine the structure by molecular replacement method, but the
> Rwork/Rfree
>
> values are huge (above 0.5) and can’t be reduced further. I suspect the
>
> obtained crystals quality and resulting processed statistics is the reason
> for
>
> the observed high Rwork/Rfree values. Are there any suggestions?
>
> All comments will be appreciated!
>
> Best,
> Chenjun Tang
>
>
>

Re: [ccp4bb] weird diffraction pattern

[Mark J van Raaij]

- which may well be caused by your cryo-protection or flash-cooling procedure.
I'd try to collect a few images at room temperature to see how good the 
crystals can be and if this procedure can be improved.
To prevent overlaps, it may help to find a way to collect the data with the 
crystal rotating around the most problematic cell axis, which tends to be the 
shortest in the crystal. Bent loops might be helpful.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser <http://www.cnb.csic.es/~mjvanraaij>.cnb.csic.es/~mjvanraaij 
<http://www.cnb.csic.es/~mjvanraaij>



> On 13 Jul 2017, at 11:13, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
> 
> You've got multiple lattices--try seeding approaches mentioned in a 
> recent/current thread.
> 
> JPK
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
> Sent: Thursday, July 13, 2017 3:56 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] weird diffraction pattern
> 
> hello everyone, 
> I would like to seek your opinion on my crystal hits. I am working on a 
> helicase 
> 
> of which the native structure is solved and the all solution statistics are 
> 
> fine. I am trying to crystallize and solve the structure of the protein/ssDNA 
> 
> complex. I recently got some hits from commercial screens using sitting drop 
> 
> vapor diffusion. After crystallization optimization, these crystals diffract 
> 
> weakly but to 3.2 Angstroms for the longer exposure time. However, when the 
> 
> crystals rotate between 120 degrees to 180 degrees, the spots become streaky
> 
> (attached), no matter the crystals are hexagonal or flaky. I have tried to 
> 
> determine the structure by molecular replacement method, but the Rwork/Rfree 
> 
> values are huge (above 0.5) and can’t be reduced further. I suspect the 
> 
> obtained crystals quality and resulting processed statistics is the reason 
> for 
> 
> the observed high Rwork/Rfree values. Are there any suggestions?
> 
> All comments will be appreciated!
> 
> Best,
> Chenjun Tang
> 
> 

Re: [ccp4bb] weird diffraction pattern

[Gerard Bricogne]

Dear Tang,

 I noticed that your diffraction images seem to have been recorded
on a 3x3 CCD detector. With this type of detector, fine slicing is
often discouraged (because of the readout noise), and yet with the two
long cell axes you have, any form of thick (or only semi-fine) slicing
would result in spot overlaps.

 What, then, was your image width? Would you have access to a
beamline with a Pilatus detector so that you could collect fine-sliced
data?

 I would tend to agree with Herman that your crystals might be
cursed with lattice translocation disorder (LTD), but you might as
well try and put every chance of surviving this on your side by making
sure that you collect fine-sliced data. LTD plus thick slicing would
give you random data along the streaky direction. Use an image width
of at most 0.1 degree (0.05 would be better) on a Pilatus, and use XDS
to process your images.


 Good luck!
 
   Gerard

--
On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun wrote:
> Hi David, 
> Thanks for your comments. Although the spots become streaky in certain 
> directions, I have processed the data in HKL3000 and imosflm, which suggested 
> the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), 
> completeness(94.8%), redundancy(4.6) are OK. When I tried to run Balbes with 
> the solved native structure, the molecular replacement solution was poor. So 
> I ran Balbes with the split domains of the native structure. Although the 
> solutions were also poor, I found the MR score of one solution above 35. On 
> the basis of this solution, I tried to run Buccaneer and the Rfree could be 
> 0.46. Unfortunately, there are four molecules in the asymmetric unit and it 
> is to hard for me to reduce the Rfree further.
> 
> All best,
> 
> Chenjun Tang

-- 

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===

[ccp4bb] AW: [ccp4bb] weird diffraction pattern

[Herman . Schreuder]

Hi Chenjun Tang,

From the images you sent, it looks like your crystal suffers from lattice 
translocation disorder. See e.g.
http://onlinelibrary.wiley.com/doi/10.1107/S0907444909025153/epdf

Calculating a native Patterson and looking for strange peaks may give some 
hints what is going on. Depending on the nature of the disorder, you may or may 
not correct for it.

Best,
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tang 
Chenjun
Gesendet: Donnerstag, 13. Juli 2017 14:21
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] weird diffraction pattern

Hi David, 
Thanks for your comments. Although the spots become streaky in certain 
directions, I have processed the data in HKL3000 and imosflm, which suggested 
the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), 
completeness(94.8%), redundancy(4.6) are OK. When I tried to run Balbes with 
the solved native structure, the molecular replacement solution was poor. So I 
ran Balbes with the split domains of the native structure. Although the 
solutions were also poor, I found the MR score of one solution above 35. On the 
basis of this solution, I tried to run Buccaneer and the Rfree could be 0.46. 
Unfortunately, there are four molecules in the asymmetric unit and it is to 
hard for me to reduce the Rfree further.

All best,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Tang Chenjun]

Hi Jacob,
I have tried seeding approaches but it didn't help.

All best,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Tang Chenjun]

Hi David, 
Thanks for your comments. Although the spots become streaky in certain 
directions, I have processed the data in HKL3000 and imosflm, which suggested 
the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), 
completeness(94.8%), redundancy(4.6) are OK. When I tried to run Balbes with 
the solved native structure, the molecular replacement solution was poor. So I 
ran Balbes with the split domains of the native structure. Although the 
solutions were also poor, I found the MR score of one solution above 35. On the 
basis of this solution, I tried to run Buccaneer and the Rfree could be 0.46. 
Unfortunately, there are four molecules in the asymmetric unit and it is to 
hard for me to reduce the Rfree further.

All best,

Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Keller, Jacob]

You've got multiple lattices--try seeding approaches mentioned in a 
recent/current thread.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Thursday, July 13, 2017 3:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] weird diffraction pattern

hello everyone, 
I would like to seek your opinion on my crystal hits. I am working on a 
helicase 

of which the native structure is solved and the all solution statistics are 

fine. I am trying to crystallize and solve the structure of the protein/ssDNA 

complex. I recently got some hits from commercial screens using sitting drop 

vapor diffusion. After crystallization optimization, these crystals diffract 

weakly but to 3.2 Angstroms for the longer exposure time. However, when the 

crystals rotate between 120 degrees to 180 degrees, the spots become streaky

(attached), no matter the crystals are hexagonal or flaky. I have tried to 

determine the structure by molecular replacement method, but the Rwork/Rfree 

values are huge (above 0.5) and can’t be reduced further. I suspect the 

obtained crystals quality and resulting processed statistics is the reason for 

the observed high Rwork/Rfree values. Are there any suggestions?

All comments will be appreciated!

Best,
Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

[Briggs, David C]

Hi,

I'd need to see more processing stats to figure out your data issues. Streaky 
spots in certain directions can be indicative of anisotropy and/or lattice 
disorders.

However, if your Rfree is above 0.5, it is likely that your molecular 
replacement solution is poor/bad/wrong.

HTH,

Dave

--
Dr David C Briggs
Hohenester Lab
Department of Life Sciences
Imperial College London
UK
http://about.me/david_briggs


From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of 唐晨骏 
<0910010...@cau.edu.cn>
Sent: Thursday, July 13, 2017 8:56:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] weird diffraction pattern

hello everyone,
I would like to seek your opinion on my crystal hits. I am working on a helicase

of which the native structure is solved and the all solution statistics are

fine. I am trying to crystallize and solve the structure of the protein/ssDNA

complex. I recently got some hits from commercial screens using sitting drop

vapor diffusion. After crystallization optimization, these crystals diffract

weakly but to 3.2 Angstroms for the longer exposure time. However, when the

crystals rotate between 120 degrees to 180 degrees, the spots become streaky

(attached), no matter the crystals are hexagonal or flaky. I have tried to

determine the structure by molecular replacement method, but the Rwork/Rfree

values are huge (above 0.5) and can’t be reduced further. I suspect the

obtained crystals quality and resulting processed statistics is the reason for

the observed high Rwork/Rfree values. Are there any suggestions?

All comments will be appreciated!

Best,
Chenjun Tang

[ccp4bb] weird diffraction pattern

[唐晨骏]

hello everyone, 
I would like to seek your opinion on my crystal hits. I am working on a 
helicase 

of which the native structure is solved and the all solution statistics are 

fine. I am trying to crystallize and solve the structure of the protein/ssDNA 

complex. I recently got some hits from commercial screens using sitting drop 

vapor diffusion. After crystallization optimization, these crystals diffract 

weakly but to 3.2 Angstroms for the longer exposure time. However, when the 

crystals rotate between 120 degrees to 180 degrees, the spots become streaky

(attached), no matter the crystals are hexagonal or flaky. I have tried to 

determine the structure by molecular replacement method, but the Rwork/Rfree 

values are huge (above 0.5) and can’t be reduced further. I suspect the 

obtained crystals quality and resulting processed statistics is the reason for 

the observed high Rwork/Rfree values. Are there any suggestions?

All comments will be appreciated!

Best,
Chenjun Tang

Re: [ccp4bb] Anisotropic diffraction

[Matthias Zebisch]

Dear Roberto,

I think you should try different special orientations of your crystals 
in the loop to find the one in which the measurable reflections stay 
away from the slow moving region (usually aligned with the beamstop 
holder, so horizontal in your image), in which reflections cannot be 
acccurately measured and are discarded by integration programs. This way 
you wont at least lose more of your precious reflections.


Generally Id recommend not to discard any measurable reflection 
irrespective of very bad overall statistics.


Best, Matthias

-
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK

Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email matth...@strubi.ox.ac.uk
Website http://www.strubi.ox.ac.uk
-

On 2/25/2015 10:07 PM, Orru, Roberto wrote:

Dear All,

My crystals are heavily affected by diffraction anisotropy as you can see in 
the images attached. I have been using the server at UCLA 
(http://services.mbi.ucla.edu/anisoscale/) to treat the datasets, but I was 
wondering if there is any suggestion on how to setup the strategy for the data 
collections and for the following integration.

Thanks in advance,
Roberto

Re: [ccp4bb] Odd diffraction

[Michael James]

Dear Fang Lu,
These spots are from a small molecule crystal. There is one very short
axial length (large distance between
reciprocal lattice rows)  and one quite long axis (the spots are close
together in the straight reciprocal lattice
row near the bottom of your diffraction pattern) You can measure these
distances and come up with an approximate
unit cell for the 2 dimensions from this one pattern.
It is certainly not a protein.

Michael James

On Wed, Feb 18, 2015 at 5:15 AM, Fang Lu fangluwork...@gmail.com wrote:

 Hi all,

 I got this odd diffraction. Not sure what it is, detergent or protein? Any
 ideas?

 The crystallisation condition is 2.4M Sodium Malonate.
 GF buffer contains HEGA-10,Tris, KAcetate, MgAcetate, EDTA and DTT.
 Protein size is around 100kDa.

 Thank you for your time.

 Fang

 [image: 内嵌图片 1]

Re: [ccp4bb] Odd diffraction

[Fang Lu]

The spots at the very edge is around 2.5A.

2015-02-18 12:15 GMT+00:00 Fang Lu fangluwork...@gmail.com:

 Hi all,

 I got this odd diffraction. Not sure what it is, detergent or protein? Any
 ideas?

 The crystallisation condition is 2.4M Sodium Malonate.
 GF buffer contains HEGA-10,Tris, KAcetate, MgAcetate, EDTA and DTT.
 Protein size is around 100kDa.

 Thank you for your time.

 Fang

 [image: 内嵌图片 1]

[ccp4bb] Odd diffraction

[Fang Lu]

Hi all,

I got this odd diffraction. Not sure what it is, detergent or protein? Any
ideas?

The crystallisation condition is 2.4M Sodium Malonate.
GF buffer contains HEGA-10,Tris, KAcetate, MgAcetate, EDTA and DTT.
Protein size is around 100kDa.

Thank you for your time.

Fang

[image: 内嵌图片 1]

[ccp4bb] GRC Diffraction 2014 Instruct fellowships

[Anastassis Perrakis]

Dear all,

Unfortunately something went wrong in email archiving, and I recall receiving 
more applications from specific people, than what are now in my mailbox. May I 
kindly ask the people that did send an application, to re-send me their PDF 
file by reply to this email?

Sorry again to everybody for the double posting and the rather silly error on 
my side -

Tassos

[ccp4bb] IUCr Diffraction Data Deposition Working Group

[Jrh Gmail]

Dear Colleagues,
We wish to let you know that the Triennial report for 2011 to 2014 on 
diffraction data deposition matters, prepared by the IUCr Diffraction Data 
Deposition Working Group (DDD WG) is now available at:-
http://forums.iucr.org/viewtopic.php?f=21t=343
Best wishes,

John, Brian and Tom 

John Helliwell Chair of the WG;
Brian McMahon Co-Chair of the WG;
Tom Terwilliger Member representing the IUCr Commission on Biological 
Macromolecules

Re: [ccp4bb] Strange diffraction

[Dominika Borek]

Small unit cell and strong diffraction -- I agree with Artem.

D.

Muhammed bashir Khan wrote:
 Hi All;
 I have a strange diffraction pattern from a membrane protein in one of
the
 PEG containing conditions. Could somebody suggest/comments about this
diffraction pattern. Please find the diffraction image attached.
According
 to my experience these are protein crystals but gives a strange
 diffraction.
 Thanks for your help
 Bashir


Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-6378 (phone) *** 214-645-6353 (fax)

[ccp4bb] Pittsburgh Diffraction Conference: registration extended to August 21, 2013

[V Yee]

Dear colleagues,

This is a reminder that the 71st Pittsburgh Diffraction Conference will be
held at the Hauptman-Woodward Medical Research Institute in Buffalo, NY on
September 18-20, 2013.  Program topics include crystallization approaches
for recalcitrant proteins and protein complexes, macromolecular design and
DNA nanotechnology, technology developments for diffraction methods, and
small molecule studies.  There will also be a number of vendors displaying
their products.

Additional information for the Conference can be found at
www.pittdifsoc.org/PDC_2013/index.htm.  We especially encourage students
and postdocs to attend.  There are currently several speaking slots still
available to be selected from submitted abstracts.

Registration is $75 for students and postdocs and $150 for others, and will
cover all meals during the meeting including the September 18 evening
opening reception and September 19 banquet.  The *registration
deadline*has been extended to
*August 21, 2013*.  Please reserve before the  *hotel deadline* of *August
21* in order to obtain the discounted rate.

To register:  www.pittdifsoc.org/PDC_2013/registration.htm

Housing info:  www.pittdifsoc.org/PDC_2013/accommodations.htm

Program:  www.pittdifsoc.org/PDC_2013/schedule.htm

For more information, please contact the organizers at
pdiffract...@hwi.buffalo.edu.

Re: [ccp4bb] Improve diffraction ...any ideas?

[Joseph Cockburn]

Hi Urmi,
When you say antibody you mean Fab fragments? If so, bear in mind that
Fab fragments can be quite flexible about the region inbetween the
variable and constant domains, which may be detrimental to the quality of
your crystals ... in this case, further to the advice of others on here,
you might consider engineering an ScFv construct for your antibody. The
constant domains of the antibody are not usually involved in antigen
binding, so the scFv should bind to the antigen in exactly the same way as
the Fab, but being less flexible it might give you better crystals.
Hope that helps,
Joe




 Hi,

 I am working on a protein antibody complex which readily crystallizes
 (crystals form overnight and grow over 2-3 days) in 0.1M Bicine pH 9, 10 %
 PEG8000. The crystals are chunky - shaped like a parallelogram but they
 diffract poorly to about 8 Å.

 I have tried the following to improve diffraction:
 1.Screen different temperatures 4°C  - crystals have bad form and 10°C
 crystals grow slower but diffraction does not improve.
 2.I have done an additive screen – A few hits came up like Yttrium
 Chloride and Acetonitrile but they don’t improve diffraction either
 3.I have tried streak seeding this does not help either
 4.Tested different cryo protectants – MPD, PEG400, Ethylene glycol and
 glycerol - 10 - 15% glycerol seems to work best
 5.Not sure if cryo protectant affects diffraction in this case – I will
 look at room temp diffraction soon to rule this out.
 6.Typical diffraction images attached

 Does anyone have suggestions on what I could try to improve diffraction of
 my crystals?



 Urmi Dhagat
 St Vincent's Institute

[ccp4bb] AW: [ccp4bb] Improve diffraction ...any ideas?

[Herman . Schreuder]

Dear Urmi,

My first question, did you collect a full data set at a synchrotron and 
processed this data? I think your diffraction is not as bad as you think it is, 
and you may get 3-3.5 Å data from it. I asume the crystal structure of the 
antigen is known and even with 4.5 Å data you could run molecular replacement 
to define the epitope, which usually is already very important information. 
You could also try to collect data from a very small crystal. When there is 
long-range disorder, small crystals may diffract better. Some microfocus 
beamlines have the possibility to scan the crystal, to find the region in the 
crystal with best diffraction. Local differences within a crystal can be 
dramatic.

Some suggestions for crystallization:
Add cryoprotectant to your crystallization setup, so you can freeze your 
crystal directly from the drop where it grew and it does not get any shocks 
when adding cryoprotectant after it is grown. Also, as you said, test 
diffraction with unfrozen crystals.
Reduce the protein concentration to slow down crystal growth, maybe combined 
with seeding.
Add some trypsin to your crystallization drop to maybe clip off some flexible 
loops.

Good luck!
Herman
 

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Urmi 
Dhagat
Gesendet: Freitag, 24. Mai 2013 04:21
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Improve diffraction ...any ideas?

Hi,

I am working on a protein antibody complex which readily crystallizes (crystals 
form overnight and grow over 2-3 days) in 0.1M Bicine pH 9, 10 % PEG8000. The 
crystals are chunky - shaped like a parallelogram but they diffract poorly to 
about 8 Å.

I have tried the following to improve diffraction:
1.  Screen different temperatures 4°C  - crystals have bad form and 10°C 
crystals grow slower but diffraction does not improve.
2.  I have done an additive screen - A few hits came up like Yttrium 
Chloride and Acetonitrile but they don't improve diffraction either
3.  I have tried streak seeding this does not help either
4.  Tested different cryo protectants - MPD, PEG400, Ethylene glycol and 
glycerol - 10 - 15% glycerol seems to work best
5.  Not sure if cryo protectant affects diffraction in this case - I will 
look at room temp diffraction soon to rule this out.
6.  Typical diffraction images attached 

Does anyone have suggestions on what I could try to improve diffraction of my 
crystals?



Urmi Dhagat
St Vincent's Institute

Re: [ccp4bb] Improve diffraction ...any ideas?

[Patrick Shaw Stewart]

Use random microseeding to pick up new conditions, and work with those.

See http://www.douglas.co.uk/mms.htm and
http://www.douglas.co.uk/MMS_proc.htm for theory, references and practical
details



On 24 May 2013 03:20, Urmi Dhagat udha...@svi.edu.au wrote:

 Hi,

 I am working on a protein antibody complex which readily crystallizes
 (crystals form overnight and grow over 2-3 days) in 0.1M Bicine pH 9, 10 %
 PEG8000. The crystals are chunky - shaped like a parallelogram but they
 diffract poorly to about 8 Å.

 I have tried the following to improve diffraction:
 1.  Screen different temperatures 4°C  - crystals have bad form and
 10°C crystals grow slower but diffraction does not improve.
 2.  I have done an additive screen – A few hits came up like Yttrium
 Chloride and Acetonitrile but they don’t improve diffraction either
 3.  I have tried streak seeding this does not help either
 4.  Tested different cryo protectants – MPD, PEG400, Ethylene glycol
 and glycerol - 10 - 15% glycerol seems to work best
 5.  Not sure if cryo protectant affects diffraction in this case – I
 will look at room temp diffraction soon to rule this out.
 6.  Typical diffraction images attached

 Does anyone have suggestions on what I could try to improve diffraction of
 my crystals?



 Urmi Dhagat
 St Vincent's Institute





-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] Improve diffraction ...any ideas?

[Patrick Shaw Stewart]

Rajiv, I don't quite get your idea.  Once the crystals of the single
proteins have grown, you can't soak the other protein in, can you?  Or do
you mean something else?

Umri, if you do get crystals of one of the components it's well worth
trying cross-seeding into the complex, again using random screens.  There
are a few examples where this has worked, particularly with antibodies.

Patrick


On 24 May 2013 06:43, Rajiv K Bedi rkn...@essex.ac.uk wrote:

 Dear Umri,

 I think the main problem is co-crystallization.

 What I would do is crystallize protein and antibody separately and then
 soak protein crystals into reservoir solution containing antibody or vice
 versa.
 And do try to get crystals from different conditions which may alter the
 space group and thereby improve diffraction quality, hopefully.

 All the best,
 Rajiv




-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] Improve diffraction ...any ideas?

[Oganesyan, Vaheh]

I think this is an advice not to follow.

 Vaheh




-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajiv K 
Bedi
Sent: Friday, May 24, 2013 1:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Improve diffraction ...any ideas?

Dear Umri,

I think the main problem is co-crystallization.

What I would do is crystallize protein and antibody separately and then soak 
protein crystals into reservoir solution containing antibody or vice versa.
And do try to get crystals from different conditions which may alter the space 
group and thereby improve diffraction quality, hopefully.

All the best,
Rajiv
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Re: [ccp4bb] Improve diffraction ...any ideas?

[Rajiv K Bedi]

I think you can soak another protein into a protein crystal if it is small 
enough to pass through water channels, I guess.

More info:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483499/

Re: [ccp4bb] Improve diffraction ...any ideas?

[Patrick Shaw Stewart]

Hello Scott

Setting up rMMS by hand works fine, but it's a bit slow and uses more
protein and (sometimes much more important!) more seed stock.

We recommend using a Hamilton syringe, preferably with a rounded needle, to
set up by hand.  1.0 protein + 0.7 reservoir solution + 0.3 seed stock
works well.  Dispense the protein and reservoir solution first, then add
the seed stock   You can clean the needle by passing it through the
reservoir just before you dispense seed stock.  It's surprising how
accurately you can dispense the seed like that with a syringe and your
fingers.

I can't say whether dispensing by robot or by hand gives better results.
 The most productive group that I know that used this method had great
success by hand before started using a robot, so I'm sure that both work
well.

Bear in mind that you're likely to get showers of small crystals at first
when you use this method.  So you will probably need to dilute the seed
stock.  What works extremely well for this is our new Combinatorial
script.  Here you arrange the hits in columns, and add a different seed
stock to each row.  Make a dilution series from neat seed stock to say a
1:100,000 dilution.  Add the most dilute seed stock to the first row, the
next most dilute to the second and so on.  Its a really quick way to get
1-5 crystals per well, and you can easily set up a whole plate with almost
the same number of crystals per well.  We use the robot to do this but I'm
sure it would be easy to do the same thing by hand.

Best wishes

Patrick



On 24 May 2013 13:46, Scott wrote:

 Dear Patrick,

  Have you had better optimization using MMS by setting up trays with a
 robot or into
 larger sitting drops by hand?

  Thank you for your suggestions.

  Cheers,

  Scott


   



  On May 24, 2013, at 8:01 AM, Patrick Shaw Stewart patr...@douglas.co.uk
  wrote:


  Use random microseeding to pick up new conditions, and work with those.

  See http://www.douglas.co.uk/mms.htm and
 http://www.douglas.co.uk/MMS_proc.htm for theory, references and
 practical details



 On 24 May 2013 03:20, Urmi Dhagat udha...@svi.edu.au wrote:

 Hi,

 I am working on a protein antibody complex which readily crystallizes
 (crystals form overnight and grow over 2-3 days) in 0.1M Bicine pH 9, 10 %
 PEG8000. The crystals are chunky - shaped like a parallelogram but they
 diffract poorly to about 8 Å.

 I have tried the following to improve diffraction:
 1.  Screen different temperatures 4°C  - crystals have bad form and
 10°C crystals grow slower but diffraction does not improve.
 2.  I have done an additive screen – A few hits came up like Yttrium
 Chloride and Acetonitrile but they don’t improve diffraction either
 3.  I have tried streak seeding this does not help either
 4.  Tested different cryo protectants – MPD, PEG400, Ethylene glycol
 and glycerol - 10 - 15% glycerol seems to work best
 5.  Not sure if cryo protectant affects diffraction in this case – I
 will look at room temp diffraction soon to rule this out.
 6.  Typical diffraction images attached

 Does anyone have suggestions on what I could try to improve diffraction
 of my crystals?



 Urmi Dhagat
 St Vincent's Institute





  --
  patr...@douglas.co.ukDouglas Instruments Ltd.
  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
  Directors: Peter Baldock, Patrick Shaw Stewart

  http://www.douglas.co.uk
  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
  Regd. England 2177994, VAT Reg. GB 480 7371 36








-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] Improve diffraction ...any ideas?

[Rajiv K Bedi]

Dear Umri,

I think the main problem is co-crystallization.

What I would do is crystallize protein and antibody separately and then soak 
protein crystals into reservoir solution containing antibody or vice versa.
And do try to get crystals from different conditions which may alter the space 
group and thereby improve diffraction quality, hopefully.

All the best,
Rajiv

Re: [ccp4bb] Strange diffraction image

[Jan Dohnalek]

Could be an organic crystal - what's the resoution of the lowest order
reflections?

Jan D.


On Fri, Oct 12, 2012 at 8:11 AM, Chang Qing robie0...@gmail.com wrote:

 Hi, everyone:

 I just got some strange diffraction images from crystals with
 triangular pyramid shape. I think this should not be protein
 diffraction. I never saw so strange images like this. Does anyone know
 what it is? Is it a kind of salt diffraction?
 Thank you very much

 Chang




-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Chang Qing]

Hi,
Thanks for answering my question.
I think I'd better provide more informations. These four images were
taken from one crystals. The distance of image1-2 is 250mm, and
image3-4 is 100mm. I checked more than 10 crystals and results were
similar. The spots look very large. The lowest resolution is about 6A.
As my protein can hydrolyze ATP, so protein buffer with 5mM of ATP.
There is 0.2M of MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl
can improve quality of crystals. I also setup control, in which target
protein was not added, and could get nothing in it. I don't think it
is a protein crystal. But salt spot should not be so large. And the
rings are not just ice-ring. As I got crystal first in hampton crystal
screen kit with MgCl2, TrisHCl and PEG4,000, there are only rings in
images from 5-6A to about 3A.

2012/10/12 THOMPSON Andrew andrew.thomp...@synchrotron-soleil.fr:
 Hi Chang
 No mention of the resolution limit / oscillation range (I think I can see an 
 ice ring, so I would guess 2.5 A?), but it looks like salt to me, with some 
 weaker satellite peaks that may be something weird like an incommensurate 
 phase.
 Did you try to index?
 Cheers
 Andy
 
 De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang Qing 
 [robie0...@gmail.com]
 Date d'envoi : vendredi 12 octobre 2012 08:11
 À : CCP4BB@JISCMAIL.AC.UK
 Objet : [ccp4bb] Strange diffraction image

 Hi, everyone:

 I just got some strange diffraction images from crystals with
 triangular pyramid shape. I think this should not be protein
 diffraction. I never saw so strange images like this. Does anyone know
 what it is? Is it a kind of salt diffraction?
 Thank you very much

 Chang

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Chang,

What makes you think spots from salt crystals should not be as large?
You have got an ordinary small molecule crystal  (or probably a
cluster of them) in the beam, with a unit cell somewhat bigger than
that of ice judging by the extra real ice rings you've got.
Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is
very unsoluble http://en.wikipedia.org/wiki/Solubility_table.

Best,
Tim

On 10/12/2012 09:29 AM, Chang Qing wrote:
 Hi, Thanks for answering my question. I think I'd better provide
 more informations. These four images were taken from one crystals.
 The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked
 more than 10 crystals and results were similar. The spots look very
 large. The lowest resolution is about 6A. As my protein can
 hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of
 MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve
 quality of crystals. I also setup control, in which target protein
 was not added, and could get nothing in it. I don't think it is a
 protein crystal. But salt spot should not be so large. And the 
 rings are not just ice-ring. As I got crystal first in hampton
 crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only
 rings in images from 5-6A to about 3A.
 
 2012/10/12 THOMPSON Andrew
 andrew.thomp...@synchrotron-soleil.fr:
 Hi Chang No mention of the resolution limit / oscillation range
 (I think I can see an ice ring, so I would guess 2.5 A?), but it
 looks like salt to me, with some weaker satellite peaks that may
 be something weird like an incommensurate phase. Did you try to
 index? Cheers Andy  De :
 CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang
 Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre
 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange
 diffraction image
 
 Hi, everyone:
 
 I just got some strange diffraction images from crystals with 
 triangular pyramid shape. I think this should not be protein 
 diffraction. I never saw so strange images like this. Does anyone
 know what it is? Is it a kind of salt diffraction? Thank you very
 much
 
 Chang
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
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Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Nicolas Foos]

Dear Chang,

i have seen ATP diffraction, it's not very different of your image. 
Maybe you have only ATP in your crystals?


Best regard

Nicolas

Le 12/10/12 14:56, Chang Qing a écrit :

Dear Tim

I think your explanation is logical. But I tried ADP as ligand first
and got crystals and diffraction. ATP in additive kit was found to
improve the quality of crystals from cluster to single crystal. CsCl
can go on improving the quality and finally I got crystals like this.
Is it possible that I get some strange crystals such as CsMgCl3 or
something else?
Best regard
Chang

-- Forwarded message --
From: Tim Gruene t...@shelx.uni-ac.gwdg.de
Date: 2012/10/12
Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image
To: Chang Qing robie0...@gmail.com
抄送： CCP4BB@jiscmail.ac.uk


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Chang,

What makes you think spots from salt crystals should not be as large?
You have got an ordinary small molecule crystal  (or probably a
cluster of them) in the beam, with a unit cell somewhat bigger than
that of ice judging by the extra real ice rings you've got.
Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is
very unsoluble http://en.wikipedia.org/wiki/Solubility_table.

Best,
Tim

On 10/12/2012 09:29 AM, Chang Qing wrote:

Hi, Thanks for answering my question. I think I'd better provide
more informations. These four images were taken from one crystals.
The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked
more than 10 crystals and results were similar. The spots look very
large. The lowest resolution is about 6A. As my protein can
hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of
MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve
quality of crystals. I also setup control, in which target protein
was not added, and could get nothing in it. I don't think it is a
protein crystal. But salt spot should not be so large. And the
rings are not just ice-ring. As I got crystal first in hampton
crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only
rings in images from 5-6A to about 3A.

2012/10/12 THOMPSON Andrew
andrew.thomp...@synchrotron-soleil.fr:

Hi Chang No mention of the resolution limit / oscillation range
(I think I can see an ice ring, so I would guess 2.5 A?), but it
looks like salt to me, with some weaker satellite peaks that may
be something weird like an incommensurate phase. Did you try to
index? Cheers Andy  De :
CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang
Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre
2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange
diffraction image

Hi, everyone:

I just got some strange diffraction images from crystals with
triangular pyramid shape. I think this should not be protein
diffraction. I never saw so strange images like this. Does anyone
know what it is? Is it a kind of salt diffraction? Thank you very
much

Chang

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image

[Chang Qing]

Dear Nicolas

ATP crystals is a reasonable answer. Thank you very much.

Best regard

Chang

2012/10/12 Nicolas Foos nicolas.f...@afmb.univ-mrs.fr:
 Dear Chang,

 i have seen ATP diffraction, it's not very different of your image. Maybe
 you have only ATP in your crystals?

 Best regard

 Nicolas

 Le 12/10/12 14:56, Chang Qing a écrit :

 Dear Tim

 I think your explanation is logical. But I tried ADP as ligand first
 and got crystals and diffraction. ATP in additive kit was found to
 improve the quality of crystals from cluster to single crystal. CsCl
 can go on improving the quality and finally I got crystals like this.
 Is it possible that I get some strange crystals such as CsMgCl3 or
 something else?
 Best regard
 Chang

 -- Forwarded message --
 From: Tim Gruene t...@shelx.uni-ac.gwdg.de
 Date: 2012/10/12
 Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image
 To: Chang Qing robie0...@gmail.com
 抄送： CCP4BB@jiscmail.ac.uk


 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Chang,

 What makes you think spots from salt crystals should not be as large?
 You have got an ordinary small molecule crystal  (or probably a
 cluster of them) in the beam, with a unit cell somewhat bigger than
 that of ice judging by the extra real ice rings you've got.
 Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is
 very unsoluble http://en.wikipedia.org/wiki/Solubility_table.

 Best,
 Tim

 On 10/12/2012 09:29 AM, Chang Qing wrote:

 Hi, Thanks for answering my question. I think I'd better provide
 more informations. These four images were taken from one crystals.
 The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked
 more than 10 crystals and results were similar. The spots look very
 large. The lowest resolution is about 6A. As my protein can
 hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of
 MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve
 quality of crystals. I also setup control, in which target protein
 was not added, and could get nothing in it. I don't think it is a
 protein crystal. But salt spot should not be so large. And the
 rings are not just ice-ring. As I got crystal first in hampton
 crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only
 rings in images from 5-6A to about 3A.

 2012/10/12 THOMPSON Andrew
 andrew.thomp...@synchrotron-soleil.fr:

 Hi Chang No mention of the resolution limit / oscillation range
 (I think I can see an ice ring, so I would guess 2.5 A?), but it
 looks like salt to me, with some weaker satellite peaks that may
 be something weird like an incommensurate phase. Did you try to
 index? Cheers Andy  De :
 CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang
 Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre
 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange
 diffraction image

 Hi, everyone:

 I just got some strange diffraction images from crystals with
 triangular pyramid shape. I think this should not be protein
 diffraction. I never saw so strange images like this. Does anyone
 know what it is? Is it a kind of salt diffraction? Thank you very
 much

 Chang

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

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 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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[ccp4bb] Pittsburgh Diffraction Conference 2012

[Smith, Clyde]

The 70th Pittsburgh Diffraction Conference will be held at SSRL between 
September 30th and October 2nd 2012 and will feature 2 full days of lectures 
and poster presentations. The conference starts with a welcome reception on 
September 30 and there will be a banquet on the evening of October 1st. The 
conference will precede the 2012 SSRL/LCLS Users' Meeting and Workshops 
http://www-conf.slac.stanford.edu/ssrl-lcls/2012/ October 3rd - 6th. Session 
topic include:

New Science with Femtosecond Diffraction
Exciting Macromolecular Structures
New Ideas in Crystallography, and
Hybrid Methods in Macromolecular Crystallography

There will be a Keynote Address to begin the Conference on Monday October 1st 
by Prof Brian Kobilka (Stanford University) on G protein coupled receptors 
(GPCRs).  All speakers and session topics can be found at this link: 
http://www.pittdifsoc.org/PDC_2012/schedule.htm

Registration is now open (US$100 or US$20 for students and postdocs) and for 
those who register at least 2 weeks in advance you will receive a free ticket 
to the banquet. There will be an award for the best student poster so get your 
abstracts in nice and early. The abstract deadline has been extended to 
September 15. Please visit the website below to register and submit your 
abstract.

http://www.pittdifsoc.org/PDC_2012/index.htm

If you have not made your hotel reservations yet and would like to stay at the 
SLAC Guest House, please reserve your room soon.  The SLAC Guest House will 
only hold the remaining rooms that have been blocked for the PDC and Users' 
Meeting through this week.   Please specify 'Users12' or 'PDS 2012' to take 
advantage of discount rates for SLAC guests.  Visit this link for more 
information about accommodation options: 
http://www.pittdifsoc.org/PDC_2012/accommodations.htm.



-
Clyde A. Smith, Ph.D.
Senior Staff Scientist
Stanford University
Stanford Synchrotron Radiation Lab, MS 99
2575 Sand Hill Rd
Menlo Park, CA 94025 USA

ph   (650)926-8544
fax  (650)926-3292
cell (650)714-6001
smb.slac.stanford.edu

Re: [ccp4bb] Anisotropic diffraction

[Dale Tronrud]

   If the data set had P6 symmetry before anisotropic scaling it would
keep that symmetry afterwards.  If it was only P2 symmetry before, it
certainly would not have P6 afterwards.  Any anisotropic scaling I've
seen constrains the anisotropy to the lattice symmetry so symmetry
cannot be degraded via its application.

   If your data set had, in principle, P6 symmetry but was expressed in
a lower symmetry asymmetric unit and contained nonsymmetry-conforming
noise before anisotropic scaling it would also contain broken symmetry
afterwards.  The higher symmetry was not lost, it was never there to
begin with.

Dale Tronrud

On 4/28/2012 12:06 AM, Zhijie Li wrote:

Hi,

My first thought was same with David: the truncation won't change the crystal's 
space group. The symmetry of the crystal is
reflected by the symmetry of the amplitudes of many many reflections across all 
resolutions. Ellipsoidal truncation itself only
removes some very weak reflections from the outer shells. The remaining 
reflections will still have a good number of reflections
carrying the symmetry of the crystal.

However a second thought on the anisotropic scaling and B-factor correction led 
me to this scenario: suppose we have a crystal
that's really P6, but we have cowardly indexed it to a lower space group P2, 
with the 2-fold axis, b, coinciding the real 6-fold
axis. By losing the a=c restrain, the anisotropic scaling along H and L now may 
not be strictly equal (for example, could be caused
by outliers that would have been identified and filtered out if indexed 
correctly as P6), resulting in the loss of the 6-fold
symmetry in the scaled dataset. Apparently this is an artifact due to an 
improper SG assignment before the anisotropic scaling and
B-factor correction.

Just some crazy thoughts. Please correct me if I am wrong.



BTW, to Theresa: an very informative introduction on ellipsoidal truncation and 
anisotropic scaling can be found here:

http://services.mbi.ucla.edu/anisoscale/



--
From: Theresa Hsu theresah...@live.com
Sent: Friday, April 27, 2012 3:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Anisotropic diffraction


Dear crystallographers

A very basic question, for anisotropic diffraction, does data truncation with 
ellipsoidal method change the symmetry? For example,
if untruncated data is space group P6, will truncated data index as P622 or P2?

Thank you.

Theresa

Re: [ccp4bb] Anisotropic diffraction

[Zhijie Li]

Hi Chen,

I see your point now. Yes, I agree that the 80:20 method (or 75:25 as stated 
in the paper, http://www.mail-archive.com/ccp4bb@dl.ac.uk/msg01063.html) is 
a very useful technique. The fact that it does not take much effort or lead 
to uncertainties makes it very worth trying.


Here I add my two cents: when performing such optimizations, try both 
seeding and no-seeding if quantity of protein permits. If protein quantity 
is limited and the crystals are reluctant to appear under the original 
condition, then seeding is always a good idea.


Zhijie




--
From: chen c chenc...@gmail.com
Sent: Sunday, April 29, 2012 6:09 PM
To: Zhijie Li zhijie...@utoronto.ca
Subject: Re: [ccp4bb] Anisotropic diffraction


I accept your advice. In fact, this is the first time I am involved in
anisotropic issue. And I learned a lot from all the above discussion.

However, the 80:20 optimization method(an example of long-tail
theory) rather than surface mutation is what I want to emphasis in my
last email. As illustrated in the attached pdf, it defenitely deserve
a try. One more thing to mention is that this very 80:20 method can be
very versatile and  useful in optimising macromolecular crystals in
case of issues more than anistropic problem.

best regards
chen



2012/4/30 Zhijie Li zhijie...@utoronto.ca:

Hi Chen,

It is a reality that a usable protein dataset could take years of hard 
work
to obtain. Compared to problems such as twining, bad diffraction 
patterns,

excessive mosaicity, low resolution, weak, noisy anomalous signal, etc.,
anisotropic diffraction should probably be regarded most benign. There is
nothing wrong with publishing a properly treated anisotropic dataset. 
Then

why risking another year trying to find a better mutant? There is no
guarantee that the mutants would work better, or even work.

Unless the crystal is naturally isotropic, such as that it is in a cubic
space group, the diffraction of protein crystals will probably always be
more or less anisotropic. This only reflects the fact that the crystal
packing is indeed anisotropic, consequently the movements of the Unit 
cell

is anisotropic. It does not mean that there would be defects in the
resulting structure. For instance, a 3A isotropic dataset, and a 2.5-2A
anisotropic dataset, which one is going to give a better description of 
the

protein?

Zhijie


--
From: chen c chenc...@gmail.com
Sent: Sunday, April 29, 2012 5:03 AM
To: Zhijie Li zhijie...@utoronto.ca

Subject: Re: [ccp4bb] Anisotropic diffraction


If we might be able to eliminate the anisotropic diffraction issue,
which might mean and reflect defect in structure. Why not just
restrain our thought to solve this question by data processing, etc?

chen

2012/4/28 Zhijie Li zhijie...@utoronto.ca:


Hi Cheng,

This paper looks quite irrelevant to Theresa's question.

Zhijie



--
From: chen c chenc...@gmail.com
Sent: Friday, April 27, 2012 10:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Anisotropic diffraction



Birtley and Curry used a novel optimization method, in their paper
Crystallization of foot-and-mouth disease virus 3C protease: surface
mutagenesis and a novel crystal-optimization strategy, which might be
inspiring for you.



在 2012年4月28日 上午3:21，David Schuller dj...@cornell.edu 写道：



Anisotropic truncation should have no effect on the space group
symmetry.



On 04/27/12 15:18, Theresa Hsu wrote:




Dear crystallographers

A very basic question, for anisotropic diffraction, does data
truncation
with ellipsoidal method change the symmetry? For example, if
untruncated
data is space group P6, will truncated data index as P622 or P2?

Thank you.

Theresa






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






--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn

北京市海淀区清华大学生命科学馆201-212室
邮编：100084








--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn

北京市海淀区清华大学生命科学馆201-212室
邮编：100084







--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn

北京市海淀区清华大学生命科学馆201-212室
邮编：100084

Re: [ccp4bb] Anisotropic diffraction

[Zhijie Li]

Hi,

My first thought was same with David: the truncation won't change the 
crystal's space group. The symmetry of the crystal is reflected by the 
symmetry of the amplitudes of many many reflections across all resolutions. 
Ellipsoidal truncation itself only removes some very weak reflections from 
the outer shells. The remaining reflections will still have a good number of 
reflections carrying the symmetry of the crystal.


However a second thought on the anisotropic scaling and B-factor correction 
led me to this scenario: suppose we have a crystal that's really P6, but we 
have cowardly indexed it to a lower space group P2, with the 2-fold axis, b, 
coinciding the real 6-fold axis. By losing the a=c restrain, the anisotropic 
scaling along H and L now may not be strictly equal (for example, could be 
caused by outliers that would have been identified and filtered out if 
indexed correctly as P6), resulting in the loss of the 6-fold symmetry in 
the scaled dataset. Apparently this is an artifact due to an improper SG 
assignment before the anisotropic scaling and B-factor correction.


Just some crazy thoughts. Please correct me if I am wrong.



BTW, to Theresa: an very informative introduction on ellipsoidal truncation 
and anisotropic scaling can be found here:


http://services.mbi.ucla.edu/anisoscale/



--
From: Theresa Hsu theresah...@live.com
Sent: Friday, April 27, 2012 3:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Anisotropic diffraction


Dear crystallographers

A very basic question, for anisotropic diffraction, does data truncation 
with ellipsoidal method change the symmetry? For example, if untruncated 
data is space group P6, will truncated data index as P622 or P2?


Thank you.

Theresa 

[ccp4bb] Anisotropic diffraction

[Theresa Hsu]

Dear crystallographers

A very basic question, for anisotropic diffraction, does data truncation with 
ellipsoidal method change the symmetry? For example, if untruncated data is 
space group P6, will truncated data index as P622 or P2?

Thank you.

Theresa

Re: [ccp4bb] Anisotropic diffraction

[David Schuller]

Anisotropic truncation should have no effect on the space group symmetry.


On 04/27/12 15:18, Theresa Hsu wrote:

Dear crystallographers

A very basic question, for anisotropic diffraction, does data truncation with 
ellipsoidal method change the symmetry? For example, if untruncated data is 
space group P6, will truncated data index as P622 or P2?

Thank you.

Theresa



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

Re: [ccp4bb] Anisotropic diffraction

[chen c]

Birtley and Curry used a novel optimization method, in their paper
Crystallization of foot-and-mouth disease virus 3C protease: surface
mutagenesis and a novel crystal-optimization strategy, which might be
inspiring for you.



在 2012年4月28日 上午3:21，David Schuller dj...@cornell.edu 写道：
 Anisotropic truncation should have no effect on the space group symmetry.



 On 04/27/12 15:18, Theresa Hsu wrote:

 Dear crystallographers

 A very basic question, for anisotropic diffraction, does data truncation
 with ellipsoidal method change the symmetry? For example, if untruncated
 data is space group P6, will truncated data index as P622 or P2?

 Thank you.

 Theresa



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



-- 
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn

北京市海淀区清华大学生命科学馆201-212室
邮编：100084

Re: [ccp4bb] No diffraction

[Jesse]

This might be obvious, but make sure you washed the crystals
thoroughly before dissolving them for SDS-PAGE or mass spec

-Jesse

On Thu, Jan 26, 2012 at 10:48 AM, Katherine Sippel
katherine.sip...@gmail.com wrote:
 Might I suggest consulting the CCP4 user community wiki on the topic:

 http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality

 Good luck,

 Katherine



 On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu theresah...@live.com
 wrote:

 Dear crystallographers

 I have a protein of 90 kDa forming dimers. Crystals formed with microbatch
 and vapor diffusion method in 24 hours but no diffraction at home source.
 Dissolved crystals was confirmed to be the protein with mass spec.

 Any suggestions to improve diffraction would be welcome.

 Thanking you in advance.

 Theresa