Re: [ccp4bb] Pilatus Issues

[John Hardin]

Dear All,

Thank you for the insightful discussion and well-intentioned admonishments.
Such open discourse is beneficial to all. 

Rigaku promptly provided us with a loaner detector while our unit is being 
repaired 
and we have been VERY happy with our detector and service overall.

The original intent of my post was merely to ascertain the frequency of this 
seemingly rare issue.

Best,
John

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

[Gerard Bricogne]

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

[Gerard Bricogne]

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] Pilatus Issues

[Keller, Jacob]

Regarding daftness, it seems that the detector is wider than tall, which should 
improve the ratio of Lorentz-problematic reflections to good, fast-moving ones. 
So I assume it was a choice between that and excluding some spots in the 
gap--an appropriate calculation could be done to see whether this is 
appropriate.

I was curious about the polarization issue you mentioned: how does horizontal 
orientation speak to polarization? I don't understand the connection.

All the best,

Jacob Keller



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard 
Bricogne
Sent: Saturday, July 15, 2017 5:31 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

[John Hardin]

Thank you Gerard.

This seems to be a very valid point. 
I myself cannot fully rule out the possibility that greater minds than mine 
may present compelling arguments for installation with a horizontal gap 
orientation.
Yet… taking your point, it is admittedly difficult for me to see any advantage 
to the current orientation other than ease of installation (mounting bracket 
location).

Thank you very much for your advice.

Best,
John

Re: [ccp4bb] Pilatus Issues

[John Hardin]

Thank you for the advice.

I had hoped to ascertain the frequency of this issue amongst the user base
and perhaps learn whether there is anything at all that we users can do to 
reduce the likelihood of its reoccurrence.

I suspect that this is a rare issue and that it is likely an electronics 
problem 
and as such is probably outside of user control/influence (aside from 
maintaining proper temperature and humidity control) .

Best,
John

Re: [ccp4bb] Pilatus Issues

[Gerard Bricogne]

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

[Andreas Förster]

Dear John,

I can't answer your questions with the limited information you supply, but
I would recommend contacting the company that sold you the detector.  Most
probably that's the maker of your diffractometer.  They'll be able to help
you out.  If it's something that requires repair, they might even send you
a loan instrument while taking care of yours.  If you bought the detector
directly from Dectris, please send an email to our support team with
details.

All best.


Andreas



On Fri, Jul 14, 2017 at 6:14 PM, 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
>
>
>


-- 

Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 | 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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