Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Tim Gruene]

Dear Andreas,

the eiger2cbf code also contains a plugin. I have been using it for
at least 2 years with the LIB= keywords in XDS.

The compilation is not automatically switched on with the Makefile, but
it takes very litte adjustment to create the binary plugin-worker and
the plugin plugin.so

It works greatly.

Best,
Tim

On Mon, 4 Jan 2021 11:10:34 +0100 Andreas Förster
 wrote:

> Dear Graeme, all,
> 
> to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to
> process EIGER and EIGER2 data collected at the synchrotron, Herbert
> Bernstein created a Windows installer for Takanori Nakane's eiger2cbf
> converter.  You can find it here:
> https://github.com/nsls-ii-mx/eiger2cbf.  Documentation is at the
> very bottom.  It works for CAP.  I haven't tried to see how useful it
> is in other contexts.  It's a converter, not a plugin, but it lets
> you work with HDF5 data under Windows.
> 
> All best.
> 
> Andreas
> 
> 
> 
> On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
> graeme.win...@diamond.ac.uk> wrote:  
> 
> > Hi All,
> >
> > Sorry for the slow response - holiday season & all (I am sure many
> > of us needed a break at the end of 2020)
> >
> > Windows is currently not super well supported for xia2 / DIALS work
> > and won’t work at all for xia2 / XDS for the simple reason that XDS
> > is not available for the platform (hence absence of durin plugin
> > for Windows mentioned elsewhere in this thread)
> >
> > Your data are from 2019 I would guess from the log text
> >
> > In this case I would honestly suggest that the best method to
> > process this data is to either -
> >  - work on a UNIX based system
> > or
> >  - restage the data to Diamond and process there
> >
> > I’m happy to help (off list) with the details of this if it would
> > help
> >
> > We probably should invest some effort in properly supporting
> > Windows for xia2 / DIALS - however there are a bunch of rather
> > nasty jobs to do in making this possible and it’s never “the most
> > important thing” sorry :-(
> >
> > Happy new year & best wishes Graeme
> >
> > On 22 Dec 2020, at 16:53, Irwin Selvam <  
> > irwin.sel...@postgrad.manchester.ac.uk> wrote:  
> >
> > Hi,
> >
> > I'd like to reprocess some data that were collected on an Eiger2
> > detector at Diamond with Xia2Dials using CCP4i2's GUI. I'm running
> > CCP4i2 on a 64-bit Windows 10 machine. The data were processed
> > successfully at Diamond with no obvious pathologies, the high
> > resolution limit was just a little generous. The folder in question
> > contains a Diamond specific file (.nsx extension), two image files
> > (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've
> > tried pointing Xia2 to the folder itself (which works when
> > processing data collected on PILATUS detectors) and each of the
> > files contained therein (except the Diamond specific file). Each
> > time this results in the error " -ERROR- None:56 Error in wrapper
> > xia2_dials 0.0:: External process exited with exit code != 0
> > Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in
> > wrapper xia2_dials 0.0:: Error in checking external process after
> > completion exit status and code: 0 1". I've attached the error,
> > debug etc files for a representative 'run' to this email. Which
> > files do I need to point xia2 towards to get it to run? Any help
> > would be appreciated.
> >
> > All the best,
> >
> > Irwin
> >
> > --
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > 
> >
> >
> >
> >
> > --
> >
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
> > addressee only. If you 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 Innovation Campus, Didcot, Oxfordshire, OX11
> > 0DE, United Kingdom
> >
> >
> > --
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >  
> 
> 



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

Phone: +43-1-4277-70202

GPG Key

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Andreas Förster]

Dear Graeme, all,

to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to process
EIGER and EIGER2 data collected at the synchrotron, Herbert Bernstein
created a Windows installer for Takanori Nakane's eiger2cbf converter.  You
can find it here:  https://github.com/nsls-ii-mx/eiger2cbf.  Documentation
is at the very bottom.  It works for CAP.  I haven't tried to see how
useful it is in other contexts.  It's a converter, not a plugin, but it
lets you work with HDF5 data under Windows.

All best.

Andreas



On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Hi All,
>
> Sorry for the slow response - holiday season & all (I am sure many of us
> needed a break at the end of 2020)
>
> Windows is currently not super well supported for xia2 / DIALS work and
> won’t work at all for xia2 / XDS for the simple reason that XDS is not
> available for the platform (hence absence of durin plugin for Windows
> mentioned elsewhere in this thread)
>
> Your data are from 2019 I would guess from the log text
>
> In this case I would honestly suggest that the best method to process this
> data is to either -
>  - work on a UNIX based system
> or
>  - restage the data to Diamond and process there
>
> I’m happy to help (off list) with the details of this if it would help
>
> We probably should invest some effort in properly supporting Windows for
> xia2 / DIALS - however there are a bunch of rather nasty jobs to do in
> making this possible and it’s never “the most important thing” sorry :-(
>
> Happy new year & best wishes Graeme
>
> On 22 Dec 2020, at 16:53, Irwin Selvam <
> irwin.sel...@postgrad.manchester.ac.uk> wrote:
>
> Hi,
>
> I'd like to reprocess some data that were collected on an Eiger2 detector
> at Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a
> 64-bit Windows 10 machine. The data were processed successfully at Diamond
> with no obvious pathologies, the high resolution limit was just a little
> generous. The folder in question contains a Diamond specific file (.nsx
> extension), two image files (.h5), a header (.cbf), a master (.h5) and meta
> file (.h5). I've tried pointing Xia2 to the folder itself (which works
> when processing data collected on PILATUS detectors) and each of the files
> contained therein (except the Diamond specific file). Each time this
> results in the error " -ERROR- None:56 Error in wrapper xia2_dials 0.0::
> External process exited with exit code != 0 Process:
> C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials
> 0.0:: Error in checking external process after completion exit status and
> code: 0 1". I've attached the error, debug etc files for a representative
> 'run' to this email. Which files do I need to point xia2 towards to get it
> to run? Any help would be appreciated.
>
> All the best,
>
> Irwin
>
> --
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>
>
>
>
> --
>
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you 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
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>


-- 

Andreas Förster, Ph.D.
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







[image: LinkedIn]

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

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

Hi All,

Sorry for the slow response - holiday season & all (I am sure many of us needed 
a break at the end of 2020)

Windows is currently not super well supported for xia2 / DIALS work and won’t 
work at all for xia2 / XDS for the simple reason that XDS is not available for 
the platform (hence absence of durin plugin for Windows mentioned elsewhere in 
this thread)

Your data are from 2019 I would guess from the log text

In this case I would honestly suggest that the best method to process this data 
is to either -
 - work on a UNIX based system
or
 - restage the data to Diamond and process there

I’m happy to help (off list) with the details of this if it would help

We probably should invest some effort in properly supporting Windows for xia2 / 
DIALS - however there are a bunch of rather nasty jobs to do in making this 
possible and it’s never “the most important thing” sorry :-(

Happy new year & best wishes Graeme

On 22 Dec 2020, at 16:53, Irwin Selvam 
mailto:irwin.sel...@postgrad.manchester.ac.uk>>
 wrote:

Hi,

I'd like to reprocess some data that were collected on an Eiger2 detector at 
Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit 
Windows 10 machine. The data were processed successfully at Diamond with no 
obvious pathologies, the high resolution limit was just a little generous. The 
folder in question contains a Diamond specific file (.nsx extension), two image 
files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried 
pointing Xia2 to the folder itself (which works when processing data collected 
on PILATUS detectors) and each of the files contained therein (except the 
Diamond specific file). Each time this results in the error " -ERROR- None:56 
Error in wrapper xia2_dials 0.0:: External process exited with exit code != 0 
Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials 
0.0:: Error in checking external process after completion exit status and code: 
0 1". I've attached the error, debug etc files for a representative 'run' to 
this email. Which files do I need to point xia2 towards to get it to run? Any 
help would be appreciated.

All the best,

Irwin


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
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 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Dom Bellini]

Hi Irwin,

I just tried on IspyB and I was able to reprocess data collected on a September 
visit, thus you should be fine if your session was only 30/40 days ago. 

I have never tried ccp4i2 on windows, sorry I cannot comment on this (but 
xia2-dials works fine in Linux/Mac using the master.h5 file). 

As Marco suggested if you use xia2-xds make sure you have the correct plug-in 
for Eiger detector 
(https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Eiger2-Detectors.html)

BW,

D

> On 22 Dec 2020, at 20:55, Irwin Selvam 
>  wrote:
> 
> 
> Hi,
> 
> Unfortunately, the data were collected more than 30/40 days ago so I 
> requested them via TOPCAT - unless there is a way round this?
> 
> All the best,
> 
> Irwin
> From: Dom Bellini 
> Sent: 22 December 2020 18:54
> To: Irwin Selvam ; 
> CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector 
> using Xia2Dials on CCP4i2's GUI
>  
> Hi Irwin,
> 
> You should use the master.h5 file, I am not sure why that is not working. 
> However, if you collected at Diamond, it is also possible to reprocess your 
> data directly from IspyB, which is very easy and convenient if you just want 
> to reprocess with different resolution 
> https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Data-Analysis/Reprocessing-in-ISPyB.html
> 
> BW,
> 
> D
> 
>> On 22/12/2020 16:53, Irwin Selvam wrote:
>> Hi,
>> 
>> I'd like to reprocess some data that were collected on an Eiger2 detector at 
>> Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit 
>> Windows 10 machine. The data were processed successfully at Diamond with no 
>> obvious pathologies, the high resolution limit was just a little generous. 
>> The folder in question contains a Diamond specific file (.nsx extension), 
>> two image files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). 
>> I've tried pointing Xia2 to the folder itself (which works when processing 
>> data collected on PILATUS detectors) and each of the files contained therein 
>> (except the Diamond specific file). Each time this results in the error " 
>> -ERROR- None:56 Error in wrapper xia2_dials 0.0:: External process exited 
>> with exit code != 0 Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 
>> Error in wrapper xia2_dials 0.0:: Error in checking external process after 
>> completion exit status and code: 0 1". I've attached the error, debug etc 
>> files for a representative 'run' to this email. Which files do I need to 
>> point xia2 towards to get it to run? Any help would be appreciated.
>> 
>> All the best,
>> 
>> Irwin
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
> 
> -- 
> Dom Bellini, Xray Crystallography Facility (1S205)
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge Biomedical Campus
> Cambridge CB2 0QH
> Phone 01223 267839
> 
> 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:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Irwin Selvam]

Hi,

Thanks for the suggestion, does this also apply to using xia2dials within 
CCP4i2 on Windows? The GitHub link and XDSwiki only mention MacOS/Red Hat. As a 
possible workaround I might be able to get access to a Mac machine to test it 
on.

All the best,

Irwin

From: Marco Mazzorana 
Sent: 22 December 2020 19:37
To: Irwin Selvam 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using 
Xia2Dials on CCP4i2's GUI

Dear Irwin,
in addition to the very good suggestion by Dom, have you checked the Durin 
plugin for XDS is correctly installed and/or referenced when launching XDS? 
This is needed when working with HDF5 and NeXuS files generated from Eiger 
detectors at Diamond.

The plugin and the basic reference are available at 
https://github.com/DiamondLightSource/durin

Should you need further information on the processing and visualization of 
files from Eiger detectors, take a look at the online documentation at 
https://www.diamond.ac.uk/Instruments/Mx/I04/I04-Manual/Eiger2-Detectors.html

Hope this helps,
Best wishes

Marco


Il giorno mar 22 dic 2020 alle ore 17:04 Irwin Selvam 
mailto:irwin.sel...@postgrad.manchester.ac.uk>>
 ha scritto:
Hi,

I'd like to reprocess some data that were collected on an Eiger2 detector at 
Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit 
Windows 10 machine. The data were processed successfully at Diamond with no 
obvious pathologies, the high resolution limit was just a little generous. The 
folder in question contains a Diamond specific file (.nsx extension), two image 
files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried 
pointing Xia2 to the folder itself (which works when processing data collected 
on PILATUS detectors) and each of the files contained therein (except the 
Diamond specific file). Each time this results in the error " -ERROR- None:56 
Error in wrapper xia2_dials 0.0:: External process exited with exit code != 0 
Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials 
0.0:: Error in checking external process after completion exit status and code: 
0 1". I've attached the error, debug etc files for a representative 'run' to 
this email. Which files do I need to point xia2 towards to get it to run? Any 
help would be appreciated.

All the best,

Irwin



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:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Irwin Selvam]

Hi,

Unfortunately, the data were collected more than 30/40 days ago so I requested 
them via TOPCAT - unless there is a way round this?

All the best,

Irwin

From: Dom Bellini 
Sent: 22 December 2020 18:54
To: Irwin Selvam ; 
CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using 
Xia2Dials on CCP4i2's GUI

Hi Irwin,

You should use the master.h5 file, I am not sure why that is not working. 
However, if you collected at Diamond, it is also possible to reprocess your 
data directly from IspyB, which is very easy and convenient if you just want to 
reprocess with different resolution 
https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Data-Analysis/Reprocessing-in-ISPyB.html

BW,

D

On 22/12/2020 16:53, Irwin Selvam wrote:
Hi,

I'd like to reprocess some data that were collected on an Eiger2 detector at 
Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit 
Windows 10 machine. The data were processed successfully at Diamond with no 
obvious pathologies, the high resolution limit was just a little generous. The 
folder in question contains a Diamond specific file (.nsx extension), two image 
files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried 
pointing Xia2 to the folder itself (which works when processing data collected 
on PILATUS detectors) and each of the files contained therein (except the 
Diamond specific file). Each time this results in the error " -ERROR- None:56 
Error in wrapper xia2_dials 0.0:: External process exited with exit code != 0 
Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials 
0.0:: Error in checking external process after completion exit status and code: 
0 1". I've attached the error, debug etc files for a representative 'run' to 
this email. Which files do I need to point xia2 towards to get it to run? Any 
help would be appreciated.

All the best,

Irwin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1


--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Marco Mazzorana]

Dear Irwin,
in addition to the very good suggestion by Dom, have you checked the Durin
plugin for XDS is correctly installed and/or referenced when launching XDS?
This is needed when working with HDF5 and NeXuS files generated from Eiger
detectors at Diamond.

The plugin and the basic reference are available at
https://github.com/DiamondLightSource/durin

Should you need further information on the processing and visualization of
files from Eiger detectors, take a look at the online documentation at
https://www.diamond.ac.uk/Instruments/Mx/I04/I04-Manual/Eiger2-Detectors.html

Hope this helps,
Best wishes

Marco


Il giorno mar 22 dic 2020 alle ore 17:04 Irwin Selvam <
irwin.sel...@postgrad.manchester.ac.uk> ha scritto:

> Hi,
>
> I'd like to reprocess some data that were collected on an Eiger2 detector
> at Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a
> 64-bit Windows 10 machine. The data were processed successfully at Diamond
> with no obvious pathologies, the high resolution limit was just a little
> generous. The folder in question contains a Diamond specific file (.nsx
> extension), two image files (.h5), a header (.cbf), a master (.h5) and meta
> file (.h5). I've tried pointing Xia2 to the folder itself (which works
> when processing data collected on PILATUS detectors) and each of the files
> contained therein (except the Diamond specific file). Each time this
> results in the error " -ERROR- None:56 Error in wrapper xia2_dials 0.0::
> External process exited with exit code != 0 Process:
> C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials
> 0.0:: Error in checking external process after completion exit status and
> code: 0 1". I've attached the error, debug etc files for a representative
> 'run' to this email. Which files do I need to point xia2 towards to get it
> to run? Any help would be appreciated.
>
> All the best,
>
> Irwin
>
> --
>
> 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:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Dom Bellini]

Hi Irwin,

You should use the master.h5 file, I am not sure why that is not 
working. However, if you collected at Diamond, it is also possible to 
reprocess your data directly from IspyB, which is very easy and 
convenient if you just want to reprocess with different resolution 
https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Data-Analysis/Reprocessing-in-ISPyB.html 



BW,

D

On 22/12/2020 16:53, Irwin Selvam wrote:

Hi,

I'd like to reprocess some data that were collected on an Eiger2 
detector at Diamond with Xia2Dials using CCP4i2's GUI. I'm running 
CCP4i2 on a 64-bit Windows 10 machine. The data were processed 
successfully at Diamond with no obvious pathologies, the high 
resolution limit was just a little generous. The folder in question 
contains a Diamond specific file (.nsx extension), two image files 
(.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried 
pointing Xia2 to the folder itself (which works when processing data 
collected on PILATUS detectors) and each of the files contained 
therein (except the Diamond specific file). Each time this results in 
the error " -ERROR- None:56 Error in wrapper xia2_dials 0.0:: External 
process exited with exit code != 0 Process: C:\CCP4-7\7.1\bin\xia2.bat 
-ERROR- None:47 Error in wrapper xia2_dials 0.0:: Error in checking 
external process after completion exit status and code: 0 1". I've 
attached the error, debug etc files for a representative 'run' to this 
email. Which files do I need to point xia2 towards to get it to run? 
Any help would be appreciated.


All the best,

Irwin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 





--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/

[ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Irwin Selvam]

Hi,

I'd like to reprocess some data that were collected on an Eiger2 detector at 
Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit 
Windows 10 machine. The data were processed successfully at Diamond with no 
obvious pathologies, the high resolution limit was just a little generous. The 
folder in question contains a Diamond specific file (.nsx extension), two image 
files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried 
pointing Xia2 to the folder itself (which works when processing data collected 
on PILATUS detectors) and each of the files contained therein (except the 
Diamond specific file). Each time this results in the error " -ERROR- None:56 
Error in wrapper xia2_dials 0.0:: External process exited with exit code != 0 
Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials 
0.0:: Error in checking external process after completion exit status and code: 
0 1". I've attached the error, debug etc files for a representative 'run' to 
this email. Which files do I need to point xia2 towards to get it to run? Any 
help would be appreciated.

All the best,

Irwin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
Environment configuration...
Python => C:\CCP4-7\7.1\libexec\python.exe
CCTBX => C:\CCP4-7\7.1\lib\py2\site-packages
CCP4 => C:\CCP4-7\7.1
CCP4_SCR => c:\users\mfbx2is2\appdata\local\temp\tmpl7kddh
Starting directory: 
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Working directory: 
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Free space:36.58 GB
Host: E-UL-MP16WKT4
Contact: xia2.supp...@gmail.com
XIA2 0.6.467-geb301d90-dials-2.2
DIALS 2.2.5-g89235367c-release
CCP4 7.1.005
Command line: xia2.bat pipeline=dials 
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2_dials.phil
 
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
QFileSystemWatcher: skipping native engine, using only polling engine 
QFileSystemWatcher: skipping native engine, using only polling engine 
QFileSystemWatcher: failed to add paths: 
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2.txt
QFileSystemWatcher: skipping native engine, using only polling engine 
QFileSystemWatcher: skipping native engine, using only polling engine 
QFileSystemWatcher: skipping native engine, using only polling engine 
QFileSystemWatcher: skipping native engine, using only polling engine 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
runTask Script raw Input Arguments 
['C:\\CCP4-7\\7.1\\share\\ccp4i2\\bin\\runTask.py', 
'C:\\Users\\MFBX2IS2\\CCP4I2_PROJECTS\\CYP141_258_7-2_reproc\\CCP4_JOBS\\job_1\\input_params.xml']
runTask Script top_path(CCPI2dir) and __file__ variables 
C:\CCP4-7\7.1\share\ccp4i2 C:\CCP4-7\7.1\share\ccp4i2\bin\runTask.py
what is going on ? loadConfig
ccp4i2 version 1.0.2
ccp4i2 source revision 5710
Running QApplication to support asyncronous sub-processes
None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file C:\Users\MFBX2IS2\CCP4I2\db\database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
CRunPlugin.run before setupComAndLog
Starting  core.CCP4DataManager.CDataManager 0.00499987602234
Running process xia2.bat asyncronously using QProcess

PROCESSMANAGER running command:
C:\CCP4-7\7.1\bin\xia2.bat pipeline=dials 
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2_dials.phil
 
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7
 > 
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\log.txt

startQProcess process says finished -1073740940 1
Process finished: 1 exit code: -1073740940 exit status: 1 time: 09:29