Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

[Harry Powell]

Hi everyone

I should mention that DIALS is available (and the developers respond rapidly to 
any issues raised) and may also be able to do something useful with these 
images…

Harry

> On 2 Dec 2019, at 09:18, Schreuder, Herman /DE  > wrote:
> 
> Hi Almuda,
> in addition to everything that had been said, I would have a look at all the 
> images of your data set, to see if there is anything that may be causing 
> misindexing in addition to the streaky spots. ADXV has the option to play a 
> movie of a complete data set. Also, ORGX and ORGY must be accurate; as a 
> crude estimate, the error should be less than half the distance between to 
> diffraction spots. Also, where Clemens was hinting at, damaged detector 
> pixels that are not removed from the image may jeopardize the indexing.
> Best,
> Herman
>  
> Von: Almudena Ponce Salvatierra  > 
> Gesendet: Samstag, 30. November 2019 11:00
> An: Schreuder, Herman /DE  >
> Cc: CCP4BB@JISCMAIL.AC.UK 
> Betreff: Re: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS
>  
> EXTERNAL : Real sender is maps.fa...@gmail.com 
>  
> 
> Hi Herman,
>  
> thank you for your answer. Yes, my data were collected at the synchrotron, 
> however, the autoprocessing failed with some of the datasets. I have checked 
> the image headers and the XDS.INP files, trying to find any mismatches 
> concerning origin, wavelength, etc... but it seems that the information was 
> recorded properly. I am trying different origins with one of the datasets, 
> but it has not helped so far.
> 
> I will write back once I find out what the problem was.
>  
> Best wishes, 
>  
> Almudena
>  
> El vie., 29 nov. 2019 a las 14:07, Schreuder, Herman /DE 
> (mailto:herman.schreu...@sanofi.com>>) escribió:
> Dear Almu,
>  
> were your data collected at a synchrotron? Many synchrotrons run automatic 
> processing of the data being collected and it is worth looking if there is 
> some processing directory between the frames you collected. If so, these data 
> may already be quite decent, and in any case, the XDS.INP file may tell you 
> how to set the optimal processing parameters for this particular beamline.
>  
> You can also look at the refined parameters of your successful XDS run, 
> especially the ORGX and ORGY. Try to rerun XDS, using the refined parameters 
> of the successful run.
>  
> Good luck!
> Herman
>  
> Von: CCP4 bulletin board  > Im Auftrag von Almudena Ponce Salvatierra
> Gesendet: Freitag, 29. November 2019 12:48
> An: CCP4BB@JISCMAIL.AC.UK 
> Betreff: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> 
>  
> 
> Dear all,
>  
> I have some data sets that don't want to be processed :p
>  
> In one of them, when I look at IDXREF.LP I see virtually none of the found 
> spots were indexed and the reason is that they are "too far from the expected 
> position". The spots are smeary and elongated, so not the prettiest. 
>  
> I have managed to process so far only one data set with decent statistics 
> from another crystal harvested from the same drop, where the diffraction 
> spots look better.
>  
> I am trying to find in the xds wiki the keyword I should fine tune in order 
> to make those spots indexable.
>  
> Could you help me please?
>  
> Thank you very much in advance.
>  
> Best wishes,
>  
> Almu
>  
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[ccp4bb] AW: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

[Schreuder, Herman /DE]

Hi Almuda,
in addition to everything that had been said, I would have a look at all the 
images of your data set, to see if there is anything that may be causing 
misindexing in addition to the streaky spots. ADXV has the option to play a 
movie of a complete data set. Also, ORGX and ORGY must be accurate; as a crude 
estimate, the error should be less than half the distance between to 
diffraction spots. Also, where Clemens was hinting at, damaged detector pixels 
that are not removed from the image may jeopardize the indexing.
Best,
Herman

Von: Almudena Ponce Salvatierra 
Gesendet: Samstag, 30. November 2019 11:00
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS


EXTERNAL : Real sender is maps.fa...@gmail.com

Hi Herman,

thank you for your answer. Yes, my data were collected at the synchrotron, 
however, the autoprocessing failed with some of the datasets. I have checked 
the image headers and the XDS.INP files, trying to find any mismatches 
concerning origin, wavelength, etc... but it seems that the information was 
recorded properly. I am trying different origins with one of the datasets, but 
it has not helped so far.

I will write back once I find out what the problem was.

Best wishes,

Almudena

El vie., 29 nov. 2019 a las 14:07, Schreuder, Herman /DE 
(mailto:herman.schreu...@sanofi.com>>) escribió:
Dear Almu,

were your data collected at a synchrotron? Many synchrotrons run automatic 
processing of the data being collected and it is worth looking if there is some 
processing directory between the frames you collected. If so, these data may 
already be quite decent, and in any case, the XDS.INP file may tell you how to 
set the optimal processing parameters for this particular beamline.

You can also look at the refined parameters of your successful XDS run, 
especially the ORGX and ORGY. Try to rerun XDS, using the refined parameters of 
the successful run.

Good luck!
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Almudena Ponce Salvatierra
Gesendet: Freitag, 29. November 2019 12:48
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Dear all,

I have some data sets that don't want to be processed :p

In one of them, when I look at IDXREF.LP I see virtually none of the found 
spots were indexed and the reason is that they are "too far from the expected 
position". The spots are smeary and elongated, so not the prettiest.

I have managed to process so far only one data set with decent statistics from 
another crystal harvested from the same drop, where the diffraction spots look 
better.

I am trying to find in the xds wiki the keyword I should fine tune in order to 
make those spots indexable.

Could you help me please?

Thank you very much in advance.

Best wishes,

Almu



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

[Schreuder, Herman /DE]

Dear Almu,

were your data collected at a synchrotron? Many synchrotrons run automatic 
processing of the data being collected and it is worth looking if there is some 
processing directory between the frames you collected. If so, these data may 
already be quite decent, and in any case, the XDS.INP file may tell you how to 
set the optimal processing parameters for this particular beamline.

You can also look at the refined parameters of your successful XDS run, 
especially the ORGX and ORGY. Try to rerun XDS, using the refined parameters of 
the successful run.

Good luck!
Herman

Von: CCP4 bulletin board  Im Auftrag von Almudena Ponce 
Salvatierra
Gesendet: Freitag, 29. November 2019 12:48
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Dear all,

I have some data sets that don't want to be processed :p

In one of them, when I look at IDXREF.LP I see virtually none of the found 
spots were indexed and the reason is that they are "too far from the expected 
position". The spots are smeary and elongated, so not the prettiest.

I have managed to process so far only one data set with decent statistics from 
another crystal harvested from the same drop, where the diffraction spots look 
better.

I am trying to find in the xds wiki the keyword I should fine tune in order to 
make those spots indexable.

Could you help me please?

Thank you very much in advance.

Best wishes,

Almu



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