[ccp4bb] Open Positions at Rigaku

[Joseph Ferrara]

Posted on behalf of Mark Benson:

Rigaku has two open positions in the US for Single Crystal Regional Account 
Managers. Ideally, one position will be East Coast-based and the other and West 
Coast-based. However, all US locations will be considered.

Either opportunity would be an excellent choice to launch a career after 
completing a Ph.D. or postdoc at an extremely exciting time with the launch of 
our Electron Diffractometer, the Synergy-ED.

Please pass on to any potentially interested candidates in your groups or to 
collaborators in the US.

For informal discussions, please contact Mark: 
mark.ben...@rigaku.com

East
https://www.rigaku.com/job/rigaku-americas-corporation/east-coast-regional-account-manager-us

West
https://www.rigaku.com/job/rigaku-oxford-diffraction-rigaku-americas-corporation/west-coast-regional-account-manager-us



Joseph D. Ferrara, Ph.D., NREMT
CSO, Rigaku Americas Corporation
Deputy Director, X-ray Research Laboratory, Rigaku Corporation
Vice-Chair, US National Committee for Crystallography
Treasurer, Council of Scientific Society Presidents

[cid:image001.png@01D82E4B.180BEFD0]

 Rigaku Americas Corporation
 9009 New Trails Drive
 The Woodlands, TX 77381 USA
 T: +1 (281) 362 2300 x168
 F: +1 (281) 364 3628
 Privacy * 
Terms * 
Disclaimer
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Joseph Ferrara]

When using Xe derivatization for SAD phasing, we (mostly Jim Pflugrath) used 
carbon tetrafluoride. CF4 has a melting point of 89.5K, just four degrees 
warmer than propane and is not flammable. 

Joe Ferrara

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Wednesday, January 26, 2022 13:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

I think the issue with propane at at least some light sources is that it is 
flammable.  Makes shipping and safety more complicated.

How hard would it be to let the propane melt off in a cryo gas stream at your 
home lab?  Then use tongs to transfer the pin into liquid N2 for handling as 
usual?  If you don't have a working N2 gas stream and are on a budget they are 
not that hard to build:
https://doi.org/10.1107/S0021889894006357

Cheers,

-James Holton
MAD Scientist


On 1/26/2022 9:25 AM, Guenter Fritz wrote:
> Dear Dom,
>
> thanks a lot. Yes, this might work sending a combipuck alongside with 
> a good bottle for the local contact.
> I was wondering whether the grippers can handle a block of propane?
>
> Best wishes,
> guenter
>> Dear Guenter,
>>
>> Would the use of vials inside combi-pucks
>> (https://www.mitegen.com/product/combipuck-system/) and some 
>> arrangements with your local contact at the other end, perhaps help 
>> with using propane remotely?
>>
>> BW,
>>
>> D
>>
>> On 26/01/2022 16:53, Guenter Fritz wrote:
>>> Dear all,
>>>
>>> we have some  delicate crystals which might benefit from freezing in 
>>> propane. In former times (when I was still travelling to the
>>> beamlines) we waited until the propane was solid in the vial and 
>>> then let the propane thaw in the cryo stream at the beamline.
>>>
>>> But how can we  do this in these days with unipucks and no manual 
>>> mounting?
>>>
>>> I was thinking about freezing in ethane and then transfer the loops 
>>> to liquid nitrogen, similarly we handle grids for cryo EM. Does 
>>> somebody has tried that? Any experience, tips & tricks would be very 
>>> welcome! Thanks in advance and best regards,
>>>
>>> Guenter
>>>
>>> 
>>> 
>>>
>>>
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>
> ##
> ##
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] saturn 724 query

[Joseph Ferrara]

Magnus,

Harry is correct about the Saturn 724. I'd like to follow up in detail but 
let's take that discussion offline to make sure the system is configured 
properly for the best results.

Cheers,

Joseph D. Ferrara, Ph.D., NREMR
CSO, Rigaku Americas Corporation
Deputy Director, X-ray Research Laboratory, Rigaku Corporation
Past President, American Crystallographic Association
Secretary-Treasurer, US National Committee for Crystallography
Treasurer, Council of Scientific Society Presidents

-Original Message-
From: CCP4 bulletin board  On Behalf Of Harry Powell - 
CCP4BB
Sent: Wednesday, October 28, 2020 5:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] saturn 724 query

Hi 

I haven’t looked at this for a few years, but I can’t see why you couldn’t; as 
far as I remember, Mosflm reads Saturn images okay.

You would probably need to do low and high resolution runs since the detector 
is (I think) only 72mm square.

Best option would be to try with something like cubic insulin or HEWL, which 
you might have on-hand.

Harry

> On 28 Oct 2020, at 10:18, Magnus Alphey 
> <4fbd1ddd2c2f-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi, 
> Does anyone know if a Rigaku Saturn 724 ccd can be used for protein crystal 
> data collection or only for small molecule ?
> Thanks
> Magnus Alphey
> 
> University of St. Andrews
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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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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--
Sent from my Android device with K-9 Mail. Please excuse my brevity.


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[ccp4bb] ACA Annual Meeting has gone virtual!

[Joseph Ferrara]

[https://acas.memberclicks.net/assets/Meeting/2020/Virtual_ACA_logo_long_1.png]

It is a pleasure to invite you to attend and submit an abstract to the 
#vACAmtg2020.
The American Crystallographic Association, Inc. (ACA) is a non-profit, 
scientific organization of over a thousand members in more than thirty-five 
countries. The ACA was established to connect scientists, and anyone interested 
in crystallography and/or structural science. Despite not being able to meet in 
person in 2020, we are excited to host our annual meeting virtually this year.
The theme of #vACAmtg2020 is "Training the Next Generation".
1.1.4 & 1.2.2 Microcrystal Electron Diffraction (MicroED) - Small Molecule & 
Macromolecules
1.2.3 Communicating Science to the Public
1.2.5 In situ / operando: From Synthesis to Devices
1.2.4 Advances in Fiber Diffraction
2.1.4 Frontiers in SAS
2.3.1 Would You Publish This?
1.2.1 Remote Access Facilities: What, Where & How?
2.1.2 Advances in Software Methods and Tools for Cryo-EM
3.2.3 Structural Contributions to SARS-CoV2 and the COVID-19 Pandemic
T1&2 Structural Science: New Ways to Teach the Next Generation
4.1.2 Structural Dynamics I. Protein Collective Motions Studied by X-ray 
Scattering and Diffraction
4.2.4 Physics and Chemistry of Matter Under Extreme Conditions
3.1.1 CryoEM in Pharma: Structure-based drug design beyond X-ray crystallography
4.2.2 Structural Dynamics II. Conformational Ensembles of Proteins Studied by 
Cryo-EM and X-ray Scattering
2.2.3 & 4.2.3 General Interest
3.1.4 & 3.2.4 Cool Structures: Important Science from Small Molecules
4.1.1 Methods and Tools for Crystallography and Cryo-EM Sample Preparation
3.2.3 Hot Structures
There is no fee to submit an abstract, but you must be an ACA member to submit 
an abstract or attend the meeting.  Join or renew 
today!
The deadline to submit is for an oral presentation is June 15, 2020 and June 
22, 2020 for a poster presentation.
For more information and to register to attend the meeting, visit our 
conference website at 
www.acameeting.com.
Questions?  Contact ACA 
HQ.
-The American Crystallographic Association-
Register to 
Attend
Important 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Question about small molecule crystallography

[Joseph Ferrara]

I would like to point out Rigaku has organized two sets of lectures, via Zoom 
webinar, on the practical aspects of small molecule crystallography. The first 
set of lectures started yesterday while the second set is scheduled to start 
July 6. 

The first lecture, an introduction, is available through our forum, 
www.RigakuXrayForum.com. Today's lecture will cover crystal screening and data 
collection. 

The link to register for the remaining lectures is at 
https://www2.rigaku.com/webinars-past/ and the link to register for the July 
session is at https://www2.rigaku.com/webinars. On those pages you will also 
find other webinars that may or may not be of interest to you. 

Be safe,

Joseph D. Ferrara, Ph.D., NREMR
CSO, Rigaku Americas Corporation
Deputy Director, X-ray Research Laboratory, Rigaku Corporation
Past President, American Crystallographic Association
Secretary-Treasurer, US National Committee for Crystallography
Treasurer, Council of Scientific Society Presidents
Rigaku Americas Corporation
9009 New Trails Drive  •  The Woodlands, TX 77381 USA
T: 281-362-2300  •  M: 281-222-9118  •  S: xrayjoe


-Original Message-
From: CCP4 bulletin board  On Behalf Of Tim Gruene
Sent: Tuesday, June 2, 2020 4:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Question about small molecule crystallography

Dear Francois,

provided you are not restricted to the trademark term 'microED', but open 
minded to include '3D electron crystallography', there are plenty of published 
structures of small compounds, both organic and inorganic.
Several of them date back to 2005, and include complex structures like MOFs, 
(Xiaodong Zou, Stockholm), twinned structures (Gemmi/Mugnaioli, Pisa), and 
really good quality work (Parsons/Zou).

Usually, crystals are not "present in powder", they compose the powder, in 
particular if you use products at 99.9% purity from Sigma-Aldrich 'off the 
shelf' is it was put, and such powders are not amorphous (if you read bioarxiv) 
or 'simingly amorphous' (if you read the peer-reviewed version)...

Scotch is not the same as adhesive tape, and pampers is not the same as diapers 
(c.f. also Gerard Bricogne's post on this bb, 29th April 2020).

Best,
Tim



 On Tue, 2 Jun 2020 10:52:45 +0200
hoh  wrote:

> Hi everyone
> 
> 
> Pr Tamir gonen (UCLA, los Angeles) have solved (not published) few 
> chemical compounds structures with mircoED. And, the more important is 
> that crystals were present in the powder (whatever condtions to get it 
> (preciptation, evaporation ..). I have myself test with 2 powders 
> coming from Chemists, here in Montpellier, and there were bunch of 
> nano crystals in both powders, and both diffract at 0.6 A.
> And, as the wavelenght in microED in very short  , Xds or Dials (with 
> some specifics parameters) are working well. And ,finally, you need 
> only  around 0.01ug of product to put on the grid (without blotting, 
> in dry method) with result almost warranty
> 
> So, think about microED for small molecules..
> 
> FH
> 
> 
> François Hoh
> 
> Centre de Biochimie Structurale,
> UMR 5048 CNRS, UMR 1054 INSERM
> 29, rue de navacelles
> 34090 Montpellier Cedex, France.
> Phone: +33 467 417 706
> Fax:   +33 467 417 913
> 
> 
> 



--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University 
of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] Sales Position at Rigaku Europe

[Joseph Ferrara]

Direct sales position at Rigaku Europe SE managing Germany, Switzerland and 
other territories.



The primary responsibilities are to acquire new customers while retaining and 
growing the existing customer base for all Rigaku products related to X-ray 
diffraction.



Main Duties

* Effectively communicate the value, features and benefits of Rigaku 
instruments to our existing and prospective customers.

* Drive and guide all aspects of the sales process - prospecting, arranging 
product demonstrations, quoting, negotiating and closing.

* Must be able to effectively communicate details from the customer to our 
internal resources and back again.

* Work closely with the sales and applications team to develop effective 
strategies.

* Build rapport and long-term relationships with customers.

* Coordinate responses for public tenders

* Reporting of forecast to director of sales



Experience and Skills

* Highly self-motivated.

* Ability to understand our customers' research needs.

* Experience in communicating to a scientific audience.

* Experience in customer service, applications or sales in any form of X-ray 
diffraction or related field is preferred.



Essential

* Science degree at the baccalaureate level

* Excellent people skills to interact with both colleagues and customers.

* Fluency in English is required. Fluency in German and other languages will be 
an asset.

* Must be prepared, and be able to travel without restriction both within and 
outside Europe for a significant proportion of time (approximately 50%).

* Full and clean driving license.



General Information

* Rigaku Europe SE office in Neu-Isenburg (near Frankfurt) Germany.

* Competitive Salary and Benefits

* All applications should be received before 31st May 2019.

* No recruiters or agencies please

* Europe SE is an equal opportunities employer.

* Candidates that meet the stated qualifications should send their CV and a 
cover letter to: rese-j...@rigaku.com




[Rigaku]

Joseph D. Ferrara, Ph.D., NREMR
CSO, Rigaku Americas Corporation
Deputy Director, X-ray Research Laboratory
President, American Crystallographic Association
Member-at-Large, Council of Scientific Society Presidents

Join our webinar series "X-ray CT for Materials 
Science"
Rigaku Americas Corporation
9009 New Trails Drive  *  The Woodlands, TX 77381 USA
T: 281-362-2300  *  M: 281-222-9118  *  S: xrayjoe
Privacy  *  
Terms  *  
Disclaimer


"Do one thing every day that scares you." ― Eleanor Roosevelt




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Re: [ccp4bb] Sulphur SAD at home source

[Joseph Ferrara]

Jim Pflugrath and a couple of high school interns shot a short video on halide 
quick soaks a few years back. You can find it at 
https://www.youtube.com/watch?v=45Qc3jOPaKY.

Cheers,

Joseph D. Ferrara, Ph.D.
CSO
Deputy Director, X-ray Research Laboratory
Vice President, American Crystallographic Association

Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger 
Rowlett
Sent: Tuesday, April 03, 2018 9:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sulphur SAD at home source

Iodine is ideally suited for Cu K-alpha SAD phasing, and iodide ions can 
normally be easily added by soaking crystals in potassium iodide containing 
solutions, which can be done at the time of cryopreservation. A quick lit 
search will turn up the appropriate protocols. For structural genomics work 
where MR was unsuccessful or unusable, iodide soaks were found to work as much 
as 80% of the time.

I've used iodide-soaked lysozyme for an XRD teaching lab and undergraduate 
research student training, and SAD phasing works really well on an overnight 
data collection on our Oxford Diffraction PX-ultra system. It's worth a shot, 
and very easy to do. Many proteins will tolerate soaking, especially if 
crystallized from salts.
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor Emeritus
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 4/3/2018 10:46 AM, Eleanor Dodson wrote:
Well - the S f" is only ~ 0.5 at Cu Kalpha so the signal will be very weak..
Very accurate data may get a solution but you first have to position the S 
atoms...
Much easier to try to make a heavy atom derivative!
Eleanor

On 3 April 2018 at 15:26, Manoj Saxena 
<1d16aa30e8a1-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi All,

I am writing to seek advice on doing  sulphur SAD data collection
at Cu based home source for a protein that is 12 KDa and has 6 S atoms.
I have seen some links online and some references but would be grateful if
you can share your know-how for success with this.
Like what multiplicity of data would be good to aim for and
data processing tips.
Inputs from people who have tried and failed would also be highly appreciated.

Thank you
Manoj Saxena
University of Puerto Rico

Re: [ccp4bb] protein quasicrystals?

[Joseph Ferrara]

Nakane-san,

There is also CrysAlisPro, which can handle multiple crystals and may already 
support your detector. If you send me the data, offline, I would be happy to 
pass it onto the CrysAlisPro development team for testing.

Joseph D. Ferrara, Ph.D.
CSO
Deputy Director, X-ray Research Laboratory
Vice President, American Crystallographic Association

Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> > on behalf of Yu Qiu
> >
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>

[ccp4bb] Application Scientist, Rigaku Oxford Diffraction, Wroclaw, Poland

[Joseph Ferrara]

Job: Application Scientist - Single Crystal X-ray Diffraction
Location: Wrocław, Poland
Salary: Competitive package
Closing Date: October 16, 2017

Description: 

Rigaku Oxford Diffraction is an international manufacturer of scientific 
instrumentation priding itself on being a customer relationship focused 
business whilse offering the best in engineering and software solutions. The 
advertised role will be based at Rigaku Polska, located in Wrocław, Poland.

In your role as an application scientist, you will be responsible for training 
users worldwide on the operation of their instruments and conducting 
demonstrations at our new demo facility in Poland. Your ability to produce high 
quality scientific reports tailored to the exacting standards of customers will 
be a key part of your job. As an application scientist you will be required to 
communicate our message to other scientists by way of presenting at conferences 
and user meetings. The ability for you to travel both in Europe and outside of 
Europe is essential and it is estimated that travel will be no more than 50% of 
the time.

You will become the face of Rigaku Oxford Diffraction, promoting through 
science our single crystal X-ray diffraction equipment. Your ability to share 
with others your enthusiasm will be advantageous to the business by forging 
bonds with scientists. Your knowledge of the current market situation for 
single crystal X-ray diffraction will be beneficial in helping to understand 
how to engage customers.

Main Duties:
- Working with the sales team to conduct demonstrations for customers
- Produce reports in a timely fashion after the demonstration
- Training users on software and how to best operate the hardware
- Maintaining the instrument(s) in the laboratory
- Maintaining the user forum and responding to queries
- Attending and presenting at conferences and user meetings worldwide
- Providing feedback to the software team
- Assisting with marketing activities
- Managing to completion smaller individual projects

Experience and Skills:

You will have good knowledge of using X-ray crystallography as a research tool 
and be able to engage customers in a positive and enthusiastic manner. 
Attention to detail is critical for accurate reporting of scientific facts.  

Essential
- Ph.D. in a relevant scientific field
- Experience of operating single crystal X-ray diffraction instruments
- Skilled in data processing and structure solution of single crystal 
diffraction data
- Excellent people skills to interact with both colleagues and customers
- Accuracy in delivering reports 
- Written and spoken fluency in English
- Ability to travel up to 50% of the time

Desirable
- Good knowledge of chemical crystallography preferred
- Experience of both protein and chemical crystallography would be beneficial
- Experience of maintaining single crystal X-ray diffraction instruments
- Proven experience of presenting to a scientific audience
- Written and spoken fluency in German 
- Polish language skills would be an advantage

Benefits
. Employment contract in a stable, international company
. Attractive social benefits package (private medical care, Benefit Sport card, 
group insurance)
. Motivational salary system

Please submit your cover letter and résumé in PDF only to h...@rigaku.com.


Cheers,

Joseph D. Ferrara, Ph.D.
Deputy Director, X-ray Research Laboratory
Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com

Re: [ccp4bb] Pilatus Issues

[Joseph Ferrara]

Gerard,

Good evening. 

We actually used the  vertical gap for the P300K because we found the vertical 
gap worked well enough with the extra module providing better coverage. 

The strategy algorithms we developed use a minimal number of 2theta settings 
and fill in missing data with different phi and chi or kappa settings. I can 
see where allowing the same sort of flexibility in 2theta settings might 
improve the speed and completeness of coverage.  I'll look into it.

Thank you for taking the time to think about it.

Cheers,

Joe Ferrara

-Original Message-
From: Gerard Bricogne [mailto:g...@globalphasing.com] 
Sent: Sunday, July 16, 2017 5:24 AM
To: Joseph Ferrara <joseph.ferr...@rigaku.com>
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Pilatus Issues

Dear Joe,

 On second thought, it seems to me that a vertical gap would be even better 
suited to the use of a 2theta axis than a horizontal one:
if one assumes that the 2-theta axis is parallel to the Omega axis, i.e. 
vertical, a small 2-theta offset by at least the angular width of the gap would 
suffice to fill it completely, as it would essentially amount to a horizontal 
translation. With a horizontal gap, a 2theta offset mostly slides the gap into 
itself, and therefore rescues fewer reflections from having fallen in the gap 
at 2theta.eq.0 . 

 I am probably missing some fine points that you looked into more 
thoroughly.


 With best wishes,
 
  Gerard.

--
On Sun, Jul 16, 2017 at 09:24:41AM +0100, Gerard Bricogne wrote:
> Dear Joe,
> 
>  Thank you for the insights :-) . Near-exclusive exposure to 
> synchrotron beamlines leads one to forget about 2theta axes, as they 
> are hardly ever encountered; but indeed it is a help here. Most of 
> all, I would assume that your default strategies would use several
> *crystal* orientations thanks to your quarter-Chi goniostat. That 
> would of course help fill the gap since it amounts to tilting it, but 
> even so, it still feels as if more low-resolution reflections would be 
> lost because of their proximity to the rotation axis than if the gap 
> was mounted vertically. Is that actually not the case?
> 
> 
>  With best wishes,
>  
>   Gerard.
> 
> --
> On Sun, Jul 16, 2017 at 06:19:01AM +, Joseph Ferrara wrote:
> > Gerard,
> > 
> > You are correct that a vertical gap is best when 2theta.eq.0 and we did 
> > explore orienting the Pilatus with the gap vertical early in the hardware 
> > integration process. However, we concluded that when 2theta.ne.0 at least 
> > two 2theta settings would be required to prevent systematically missing 
> > resolution shells. Since most data sets are collected with 2theta.ne.0 we 
> > decided on the horizontal gap in order to distribute the missing data 
> > evenly. Please note the direct beam is not in the gap so low resolution 
> > reflections are accessible.
> > 
> > I would also like to point that a loaner detector was provided to John a 
> > few days ago and we are working with Dectris to sort out the issue that 
> > began this discussion.
> > 
> > Cheers,
> > 
> > Joe Ferrara
> > 
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf 
> > Of Gerard Bricogne
> > Sent: Saturday, July 15, 2017 4:31 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Pilatus Issues
> > 
> > Dear John,
> > 
> >  Having just seen Andreas's message regarding the best source of 
> > support to address your enquiry, I have a further remark to make about your 
> > instrument.
> > 
> >  As this is a lab instrument, the Omega axis would be vertical, and 
> > indeed the beam stop shadow (vertical on the top module) and the diffuse 
> > shadow of the sample holder (vertical on the bottom module) would confirm 
> > this. This being the case, it is quite simply *daft* to have the gap 
> > between the two modules being horizontal. That is done on purpose on 
> > synchrotron beamlines because of the polarisation of the beam (which is why 
> > Omega is horizontal on such beamlines), but in a lab system the gap should 
> > be in the vertical direction. As currently placed in your system, this gap 
> > is cutting into perfectly good data, whereas if it were vertical instead, 
> > it would only cut out data that are getting perilouly close to the cusp 
> > anyway.
> > 
> >  You should ask the manufacturer of your diffractometer to rotate your 
> > detector by 90 degrees! Someone in the OEM world forgot about the Lorentz 
> > factor ;-) .
> > 
> > 
> >  With best wishes,
> >  
> >   Gerard.
> > 
> > --
> > On Fri, Jul 14, 2017 at 05:14:03PM +0100, John Hardin wrote:
> > > Hi,
> > > 
> > > We have recently noticed an issue with our Pilatus (biased 
> > > pixels/vertical lines).
> > > I was curious as to whether anyone else has seen this or might know what 
> > > could have caused it?
> > > 
> > > Best,
> > > John
> > > 

Re: [ccp4bb] Pilatus Issues

[Joseph Ferrara]

Gerard,

You are correct that a vertical gap is best when 2theta.eq.0 and we did explore 
orienting the Pilatus with the gap vertical early in the hardware integration 
process. However, we concluded that when 2theta.ne.0 at least two 2theta 
settings would be required to prevent systematically missing resolution shells. 
Since most data sets are collected with 2theta.ne.0 we decided on the 
horizontal gap in order to distribute the missing data evenly. Please note the 
direct beam is not in the gap so low resolution reflections are accessible.

I would also like to point that a loaner detector was provided to John a few 
days ago and we are working with Dectris to sort out the issue that began this 
discussion.

Cheers,

Joe Ferrara 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard 
Bricogne
Sent: Saturday, July 15, 2017 4:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Pilatus Issues

Dear John,

 Having just seen Andreas's message regarding the best source of support to 
address your enquiry, I have a further remark to make about your instrument.

 As this is a lab instrument, the Omega axis would be vertical, and indeed 
the beam stop shadow (vertical on the top module) and the diffuse shadow of the 
sample holder (vertical on the bottom module) would confirm this. This being 
the case, it is quite simply *daft* to have the gap between the two modules 
being horizontal. That is done on purpose on synchrotron beamlines because of 
the polarisation of the beam (which is why Omega is horizontal on such 
beamlines), but in a lab system the gap should be in the vertical direction. As 
currently placed in your system, this gap is cutting into perfectly good data, 
whereas if it were vertical instead, it would only cut out data that are 
getting perilouly close to the cusp anyway.

 You should ask the manufacturer of your diffractometer to rotate your 
detector by 90 degrees! Someone in the OEM world forgot about the Lorentz 
factor ;-) .


 With best wishes,
 
  Gerard.

--
On Fri, Jul 14, 2017 at 05:14:03PM +0100, John Hardin wrote:
> Hi,
> 
> We have recently noticed an issue with our Pilatus (biased pixels/vertical 
> lines).
> I was curious as to whether anyone else has seen this or might know what 
> could have caused it?
> 
> Best,
> John
> 

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

[Joseph Ferrara]

 On Friday 24 April 2009 11:53:27 Jacob Keller wrote:
  Aha, so I have re-invented the wheel! But I never made sense of why
 f' is
  negative--this is beautiful! Just to make sure: you are saying that
 the real
  part of the anomalous scattering goes negative because those photons
 are
  sneaking out of the diffraction pattern through absorption--
 fluorescence?
 
 I am not sure about that because.  Let's not confuse correlation with
 causality.  The negative f' is adequately explained by the Kramers-
 Kronig
 equation as being a result of the resonance interaction.
   http://www.rp-photonics.com/kramers_kronig_relations.html
 The maximum resonance is at the absorption energy, which is also the
 maximum for the fluorescence.  Both effects are because of the match
 between incident photon energy and the energy required to kick an
 electron
 out of its current orbital state.  I am uneasy saying that one effect
 causes the other effect.
 
   Ethan

There is a very good technical description in Jens Als-Nielsen's Elements
of Modern X-ray Physics in the chapter  Resonant Scattering, pg 235 ff. In
fact, there is also a good description of the breakdown of Friedel's Law and
the  MAD experiment in that chapter.

I would like to iterate Ethan's comment about resonance. The effects are not
anomalous at all, we know very well what is happening: the changes in f', f
and mu as a function of energy are all effects of the resonance of the
photon energy with transition energy of the electron. So, we really should
call it resonance scattering, not anomalous scattering.

I have to admit MRD and SRD aren't as euphonic at MAD and SAD and the change
will probably never happen.

Joe

Joseph D. Ferrara, Ph.D.
Rigaku Americas Corporation


 
  Jacob
 
  ***
  Jacob Pearson Keller
  Northwestern University
  Medical Scientist Training Program
  Dallos Laboratory
  F. Searle 1-240
  2240 Campus Drive
  Evanston IL 60208
  lab: 847.491.2438
  cel: 773.608.9185
  email: j-kell...@northwestern.edu
  ***
 
  - Original Message -
  From: Ethan Merritt merr...@u.washington.edu
  To: Jacob Keller j-kell...@md.northwestern.edu;
 CCP4BB@jiscmail.ac.uk
  Sent: Friday, April 24, 2009 1:40 PM
  Subject: Re: [ccp4bb] Reason for Neglected X-ray Fluorescence
 
 
   On Friday 24 April 2009 11:28:16 Jacob Keller wrote:
   Dear Dr. Holton and CCP4BBers,
  
   Are you saying that a resonant event is always accompanied by a
   fluorescence
   event? If that were true, wouldn't the resonant event end up
 manifesting
   as
   *negative* scattering component from the resonant atom, due to the
   elimination of an otherwise-scattered photon, this making the
 resonant
   atom
   darker than would be expected?
  
   Yes.
   That is why the real component of the scattering factor, f', is
 negative.
  
  
   --
   Ethan A Merritt
   Biomolecular Structure Center
   University of Washington, Seattle 98195-7742
  
 
 
 
 
 
 
 --
 Ethan A Merritt
 Biomolecular Structure Center
 University of Washington, Seattle 98195-7742