Re: [ccp4bb] number of frames to get a full dataset?

[Jose Brandao-Neto]

To improve both multiplicity, anomalous signal and dose-proofing from a single 
crystal - complementing the thread and papers suggested so far and thinking of 
a strategy that covers low symmetry - the excellent approach introduced at the 
SLS (Basu et al, http://scripts.iucr.org/cgi-bin/paper?S2059798319003103) to 
offset chi/kappa at each 180 degree pass done at very low dose per pass is a 
great strategy. one can exploit one crystal as much as possible by trimming the 
set later if decay is an issue. 

Other than that, multi crystal strategies come in handy with their own 
downsides, but if reproducible enough crystals are available then that route is 
a good one, too. an early reference by gumiero et al is great 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020733/)  and one of its latest 
implementations by ebrahim et al is also great 
(https://journals.iucr.org/m/issues/2019/04/00/ec5012/). 

cheers,
Jose'

===
Jose Brandao-Neto MPhil CPhys
Senior Beamline Scientist - I04-1
XChem Scientist
Diamond Light Source

jose.brandao-n...@diamond.ac.uk
+44 (0)1235 778506
===



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Re: [ccp4bb] 13th CCP4/APS Crystallographic School in the US

[Xu, Qingping]

Dear colleagues,

The 2020 CCP4 School at APS has been cancelled. Due to the pandemic, it is not 
possible to find a timeslot for the gathering at Argonne for the rest of the 
year. We are very sorry for the inconvenience.

We want to thank the registrants for their interest in the School. The 
registration information will be carried over for the next event (Let us know 
if you are no longer interested).

Hope to see everybody next year! Stay safe!

The CCP4 School at APS Organizers

From: Xu, Qingping
Sent: Wednesday, April 1, 2020 7:18 AM
To: CCP4BB@JISCMAIL.AC.UK; pheni...@phenix-online.org; 
pymol-us...@lists.sourceforge.net
Subject: RE: 13th CCP4/APS Crystallographic School in the US


Dear colleagues,



Due to the on-going pandemic, the 2020 CCP4/APS workshop (originally scheduled 
for June 15-22, 2020) is postponed. We will try to schedule the workshop at a 
later date. If no suitable date is found, the event will be cancelled. Further 
notice will be announced in the CCP4 bulletin board.  In the meantime, the 
registration site remains open. We are sorry for the inconvenience.





The CCP4/APS school organizers


From: Xu, Qingping mailto:q...@anl.gov>>
Sent: Monday, January 6, 2020 12:04 PM
To: CCP4BB@JISCMAIL.AC.UK; 
pheni...@phenix-online.org; 
pymol-us...@lists.sourceforge.net
Subject: 13th CCP4/APS Crystallographic School in the US


Dear Colleagues,

We are pleased to announce the 13th annual CCP4/APS crystallographic school 
“From data collection to structure refinement and beyond” will be held on June 
15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory 
(ANL), near Chicago, Illinois, USA. All details can be found at the school 
website: http://www.ccp4.ac.uk/schools/APS-2020/index.php.

Dates: June 15 through 22, 2020

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near 
Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic 
computing workshop. Data collection workshop includes beamline training, data 
collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M 
and Eiger 16M detectors respectively, and data processing. For data collection, 
only the participants' crystals will be used. Crystallographic computation 
workshop will feature many modern crystallographic software packages taught by 
authors and other experts. The daily schedule will be organized in three 
sections – lectures, tutorials, and hands-on (interactive trouble-shooting of 
the technical difficulties the participants face in their projects). We have 
had considerable success resolving these problems in past years, attested by 
resulting publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, 
contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career 
faculty, along with commercial/industrial researchers are encouraged to apply. 
Only about 20 applicants will be selected for participation. Participants of 
the workshop are strongly encouraged to bring their own problem data sets or 
crystals so the problems can be addressed during data collection and/or 
computation workshops.

Application: Application deadline is April 1st, 2020. To apply, visit 
https://www.ccp4.ac.uk/schools/APS-2020/application.php.

Fees: The registration for application is free but there is $500 participation 
fee for the selected academic students and $950 for industrial researchers. A 
valid credit card is required for registration, however, it will be charged 
only for students selected to participate. The students will be responsible for 
their transportation and lodging. The workshop organizers can assist in making 
lodging reservations at the Argonne Guest House. The workshop will cover all 
other expenses (including meals).


We hope to see you at the school.


Charles, Garib and Qingping



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[ccp4bb] How many microfocus beamlines are in the world?

[Murpholino Peligro]

I would like to know how many MX beamlines are micro focus?


Thanks.



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Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to 

a.  the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
b.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction) 
c.  the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.

How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

and also on page 306 in BMC.

Too much multiplicity might create duplicity…   

Cheers, BR

 

Jon Cooper

 

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au> > wrote:

I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences. 

I'm not a minimalist when it comes to data- redundancy is a good thing to have. 

cheers, tom 

 

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au   

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of 0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
  
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 >
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK   
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] number of frames to get a full dataset? 

 

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

what other factors can change n... besides symmetry and radiation damage?

 

Thanks

 

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-- 

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Application Scientist Crystallography, Area Sales Manager Asia & Pacific

Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: 
andreas.foers...@dectris.com  

DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | 
www.dectris.com  

 

 

   


  

   
 

 

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Re: [ccp4bb] How many microfocus beamlines are in the world?

[James Holton]

Define "micro focus" ?

-James Holton
MAD Scientist

On 6/24/2020 9:18 AM, Murpholino Peligro wrote:

I would like to know how many MX beamlines are micro focus?


Thanks.



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Re: [ccp4bb] How many microfocus beamlines are in the world?

[Gianluca Santoni]

Since we commonly consider nanofocus a beamline that can go below 1 micron, I 
would say anything below 1mm for the sake of uniformity.



On June 24, 2020 8:02:10 PM GMT+02:00, James Holton  wrote:
>Define "micro focus" ?
>
>-James Holton
>MAD Scientist
>
>On 6/24/2020 9:18 AM, Murpholino Peligro wrote:
>> I would like to know how many MX beamlines are micro focus?
>>
>>
>> Thanks.
>>
>>
>
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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-- 
Sent from my Android device with K-9 Mail. Please excuse my brevity.



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Re: [ccp4bb] How many microfocus beamlines are in the world?

[Jeffrey, Philip D.]

I'm fairly sure that the 300-ish micron focus on my old (and retired) Rigaku 
RuH3R home system  - a perfectly good workhorse - was consider micro-focus by 
precisely nobody.

Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Gianluca Santoni 

Sent: Wednesday, June 24, 2020 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How many microfocus beamlines are in the world?

Since we commonly consider nanofocus a beamline that can go below 1 micron, I 
would say anything below 1mm for the sake of uniformity.



On June 24, 2020 8:02:10 PM GMT+02:00, James Holton  wrote:
Define "micro focus" ?

-James Holton
MAD Scientist

On 6/24/2020 9:18 AM, Murpholino Peligro wrote:
I would like to know how many MX beamlines are micro focus?


Thanks.



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[ccp4bb] Energy minimization and explicit solvent model

[Andre LB Ambrosio]

Dear colleagues,

could you please suggest a computational tool to perform energy
minimization of a crystal structure under explicit solvent conditions (i.e,
types and concentrations of ions, pH)?

I want to observe the solvent effects on the conformational space around a
starting model, all-atom, while preserving its geometry (I guess it can be
better expressed as relaxation).

Thank you in advance.

-- 
Andre LB Ambrosio



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Re: [ccp4bb] Energy minimization and explicit solvent model

[Sorin Draga]

Dear Andre,

I am not sure what you mean by conformational space around the model, but
to answer your question: short energy minimization can be done using, for
example, deep view/swiss pdb viewer. However, I think that you are most
likely looking for a short bout of molecular dynamics, in which you can use
explicit solvent and a proper ionic envelope. There you have a few options
- GROMACS, NAMD, AMBER etc. The first 2 are free for academia, but if you
have no prior knowledge of MD it can be a little bit tricky to set the
system up correctly. Let me know if I can help further.

Best,

Sorin

On Wed, Jun 24, 2020 at 10:08 PM Andre LB Ambrosio 
wrote:

> Dear colleagues,
>
> could you please suggest a computational tool to perform energy
> minimization of a crystal structure under explicit solvent conditions (i.e,
> types and concentrations of ions, pH)?
>
> I want to observe the solvent effects on the conformational space around a
> starting model, all-atom, while preserving its geometry (I guess it can be
> better expressed as relaxation).
>
> Thank you in advance.
>
> --
> Andre LB Ambrosio
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] How many microfocus beamlines are in the world?

[Joseph Ferrara]

I agree with Phil. We did not consider sources to be "micro-focus" until we hit 
70 microns or so in projection, circa 1999 for rotating anodes and a bit 
earlier for sealed tube sources.

It was Uli Arndt's paper, Focusing optics for laboratory sources in X-ray 
crystallography, J. Appl. Cryst. (1990). 23, 161-168, that set the stage for 
micro-focus sources in the home laboratory.

Joe Ferrara

From: CCP4 bulletin board  On Behalf Of Jeffrey, Philip 
D.
Sent: Wednesday, June 24, 2020 1:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] How many microfocus beamlines are in the world?

I'm fairly sure that the 300-ish micron focus on my old (and retired) Rigaku 
RuH3R home system  - a perfectly good workhorse - was consider micro-focus by 
precisely nobody.

Phil Jeffrey
Princeton


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Gianluca Santoni 
mailto:gianluca.sant...@esrf.fr>>
Sent: Wednesday, June 24, 2020 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] How many microfocus beamlines are in the world?

Since we commonly consider nanofocus a beamline that can go below 1 micron, I 
would say anything below 1mm for the sake of uniformity.


On June 24, 2020 8:02:10 PM GMT+02:00, James Holton 
mailto:jmhol...@lbl.gov>> wrote:
Define "micro focus" ?

-James Holton
MAD Scientist
On 6/24/2020 9:18 AM, Murpholino Peligro wrote:
I would like to know how many MX beamlines are micro focus?

Thanks.



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[ccp4bb] dewar horror stories

[Patrick Loll]

Hello community,

We recently had a dry shipping dewar fail catastrophically (while en route to 
the beam line, so, major trauma). I sent it to a company that specializes in 
repair and refurbishing of cryogenic tanks, and they told me it has an internal 
leak, and hence is not reparable. I was expecting that the valve had failed, so 
the internal leak diagnosis came as a surprise.

Has anyone else had a similar experience? Any ideas about how an internal leak 
might come about? The dewar is (was) a Taylor/Wharton CX100, and it was 
traveling in its bespoke shipping case.

Thanks for any insights that might satisfy my curiosity and/or prevent future 
mishaps of this sort.

Cheers,

Pat

__

Patrick J.  Loll, PhD
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St.
Philadelphia, PA 19102-1192 USA

(215) 762-7706
pj...@drexel.edu 



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Re: [ccp4bb] How many microfocus beamlines are in the world?

[Murpholino Peligro]

That's a good point...
I was thinking that a decent crystal has a size in the hundreds of
micrometers (say 100 in a, b and c). So, with such a specimen we can use
any MX beamline.
But if the crystal is smaller (say 10 micrometers in a, b and c) You must
use a microfocus beamline.
*Please correct me if I am wrong.*
So what are the number of MX beamlines that can get useful data from
smaller crystals (as defined above)?

Thanks again

El mié., 24 de jun. de 2020 a la(s) 13:02, James Holton (jmhol...@lbl.gov)
escribió:

> Define "micro focus" ?
>
> -James Holton
> MAD Scientist
>
> On 6/24/2020 9:18 AM, Murpholino Peligro wrote:
>
> I would like to know how many MX beamlines are micro focus?
>
>
> Thanks.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
>



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Re: [ccp4bb] Energy minimization and explicit solvent model

[Andre LB Ambrosio]

Dear Sorin, many thanks for this. Very useful.

By probing the conformational space around the model, I meant to try and
predict how specific solvent conditions may (or may not) induce
rearrangement, both intra and intermolecule, within an oligomeric
multidomain protein compared to it in a crystalline state.

I will have an immediate look at the software and documentation you
recommended and may eventually reach out for extra help.

With best wishes

Andre.

Em qua., 24 de jun. de 2020 às 16:18, Sorin Draga 
escreveu:

> Dear Andre,
>
> I am not sure what you mean by conformational space around the model, but
> to answer your question: short energy minimization can be done using, for
> example, deep view/swiss pdb viewer. However, I think that you are most
> likely looking for a short bout of molecular dynamics, in which you can use
> explicit solvent and a proper ionic envelope. There you have a few options
> - GROMACS, NAMD, AMBER etc. The first 2 are free for academia, but if you
> have no prior knowledge of MD it can be a little bit tricky to set the
> system up correctly. Let me know if I can help further.
>
> Best,
>
> Sorin
>
> On Wed, Jun 24, 2020 at 10:08 PM Andre LB Ambrosio 
> wrote:
>
>> Dear colleagues,
>>
>> could you please suggest a computational tool to perform energy
>> minimization of a crystal structure under explicit solvent conditions (i.e,
>> types and concentrations of ions, pH)?
>>
>> I want to observe the solvent effects on the conformational space around
>> a starting model, all-atom, while preserving its geometry (I guess it can
>> be better expressed as relaxation).
>>
>> Thank you in advance.
>>
>> --
>> Andre LB Ambrosio
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>

-- 
Andre LB Ambrosio



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Re: [ccp4bb] dewar horror stories

[Jan Dohnalek]

We have the suspicion (after several heavy FEDEX failures) they just toss
them around ... then the neck easily breaks off.
That only explains everything we have seen with completely damaged samples,
lost, flying around the dewar etc ...
When trying to communicate seriously with FEDEX about these issues - they
even did not reply ...

Jan



On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll  wrote:

> Hello community,
>
> We recently had a dry shipping dewar fail catastrophically (while en route
> to the beam line, so, major trauma). I sent it to a company that
> specializes in repair and refurbishing of cryogenic tanks, and they told me
> it has an internal leak, and hence is not reparable. I was expecting that
> the valve had failed, so the internal leak diagnosis came as a surprise.
>
> Has anyone else had a similar experience? Any ideas about how an internal
> leak might come about? The dewar is (was) a Taylor/Wharton CX100, and it
> was traveling in its bespoke shipping case.
>
> Thanks for any insights that might satisfy my curiosity and/or prevent
> future mishaps of this sort.
>
> Cheers,
>
> Pat
>
> __
>
> Patrick J.  Loll, PhD
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St.
> Philadelphia, PA 19102-1192 USA
>
> (215) 762-7706
> pj...@drexel.edu
>
>
> --
>
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>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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