Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Lawson (JIC)]

Just to follow up on this one...

The problem was at my end, there was an issue with the upload from my iMac 
(possibly something to do with the system's proxy server settings). When I 
switched to using a PC, everything works as it should.
N.B. when providing a scaled but unmerged mtz, it is important to have the 
"Check here if the data are unmerged but already scaled ..." button checked.

Thanks to Ian and Clemens at Global Phasing for help with troubleshooting.

Dave

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk

From: CCP4 bulletin board  On Behalf Of David Waterman
Sent: 14 January 2020 11:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Hi Eleanor,

MTZ history is still useful, so from a recent xia2 run I can see (with mtzdmp):

 * HISTORY for current MTZ file :

 From DIALS 2.0.1-gb22bab67b-release, run on 2019-11-21 at 10:59:17 GMT

It isn't possible to tell that the data were actually scaled in DIALS too 
though, apart from the lack of POINTLESS and AIMLESS lines within the history. 
As Graeme says, I think there are opportunities here for more sophisticated 
tracking of provenance - certainly going back as far as telling us where and 
when the images were collected would be most useful.

Cheers
-- David


On Tue, 14 Jan 2020 at 11:04, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Not quite relevent but is there some way of stamping these files with a record 
of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but now 
with automated file naming it is hard to keep track of how a file was generated.


It seems likely that lots of Table !s do not describe the data set that was 
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:
Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme


On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[Ian Tickle]

Hi Graeme

No it looks like the problem is some network setting on David's side since
I can submit David's data to the STARANISO server with no problem.  The
only thing to be aware of is that when submitting scaled unmerged data the
checkbox "*Check* here if the data are unmerged but already scaled, ..."
must be checked.

Cheers

-- Ian


On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Dear  Dave, Star Aniso Developers,
>
> If this turns out to be because we are “missing something” i.e. there is
> an expectation on a property being present in the output files but it’s not
> there in our MTZ output, please let us know :-)
>
> Best wishes Graeme
>
> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
> wrote:
>
> Dear ccp4bb
>
> I am trying to get the staraniso server to accept a scaled but unmerged
> mtz file from DIALS processing, but it reports an “Internal Server Error”
> after thinking about it for a while. Should this be possible? The file is
> 31 MB, so not huge.
>
> It works fine for a merged mtz from DIALS, but this is not the preferred
> option and I don’t get the full statistics I need for Table 1.
>
> Thanks in advance
>
> Dave Lawson
>
> ---
>
> Prof. David M. Lawson
> Department of Biological Chemistry,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=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.
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> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Waterman]

Hi Eleanor,

MTZ history is still useful, so from a recent xia2 run I can see (with
mtzdmp):

 * HISTORY for current MTZ file :

 From DIALS 2.0.1-gb22bab67b-release, run on 2019-11-21 at 10:59:17 GMT

It isn't possible to tell that the data were actually scaled in DIALS too
though, apart from the lack of POINTLESS and AIMLESS lines within the
history. As Graeme says, I think there are opportunities here for more
sophisticated tracking of provenance - certainly going back as far as
telling us where and when the images were collected would be most useful.

Cheers
-- David


On Tue, 14 Jan 2020 at 11:04, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Not quite relevent but is there some way of stamping these files with a
> record of where they were generated ?
> I used to use my ability to read - name them myself as
> SAMPLEX-dialsprocessing-unmerged.mtz then
> SAMPLEX-dialsprocessing-unmerged-staranisod.mtz
>
> and there is an mtz feature which wrote a history with dates as well but
> now with automated file naming it is hard to keep track of how a file was
> generated.
>
>
> It seems likely that lots of Table !s do not describe the data set that
> was actually used for structure solution and deposition!
>
> Eleanor
>
> On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
> graeme.win...@diamond.ac.uk> wrote:
>
>> Dear  Dave, Star Aniso Developers,
>>
>> If this turns out to be because we are “missing something” i.e. there is
>> an expectation on a property being present in the output files but it’s not
>> there in our MTZ output, please let us know :-)
>>
>> Best wishes Graeme
>>
>> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
>> wrote:
>>
>> Dear ccp4bb
>>
>> I am trying to get the staraniso server to accept a scaled but unmerged
>> mtz file from DIALS processing, but it reports an “Internal Server Error”
>> after thinking about it for a while. Should this be possible? The file is
>> 31 MB, so not huge.
>>
>> It works fine for a merged mtz from DIALS, but this is not the preferred
>> option and I don’t get the full statistics I need for Table 1.
>>
>> Thanks in advance
>>
>> Dave Lawson
>>
>> ---
>>
>> Prof. David M. Lawson
>> Department of Biological Chemistry,
>> John Innes Centre,
>> Norwich,
>> NR4 7UH, UK.
>> Tel: +44-(0)1603-450725
>> Web: https://www.jic.ac.uk/people/david-lawson
>> Email: david.law...@jic.ac.uk
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=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/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

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

Hello Eleanor

Is that the sound of worms escaping a pot I hear in the distance? Certainly is!

Yes, this is something which was raised with a few of my colleagues at the 
study weekend and something we are discussing internally - with my facility hat 
on I think we should get to the bottom of this one - early in the year.

best wishes Graeme

On 14 Jan 2020, at 11:03, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:

Not quite relevent but is there some way of stamping these files with a record 
of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but now 
with automated file naming it is hard to keep track of how a file was generated.


It seems likely that lots of Table !s do not describe the data set that was 
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:
Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme

On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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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




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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[Eleanor Dodson]

Not quite relevent but is there some way of stamping these files with a
record of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but
now with automated file naming it is hard to keep track of how a file was
generated.


It seems likely that lots of Table !s do not describe the data set that was
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Dear  Dave, Star Aniso Developers,
>
> If this turns out to be because we are “missing something” i.e. there is
> an expectation on a property being present in the output files but it’s not
> there in our MTZ output, please let us know :-)
>
> Best wishes Graeme
>
> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
> wrote:
>
> Dear ccp4bb
>
> I am trying to get the staraniso server to accept a scaled but unmerged
> mtz file from DIALS processing, but it reports an “Internal Server Error”
> after thinking about it for a while. Should this be possible? The file is
> 31 MB, so not huge.
>
> It works fine for a merged mtz from DIALS, but this is not the preferred
> option and I don’t get the full statistics I need for Table 1.
>
> Thanks in advance
>
> Dave Lawson
>
> ---
>
> Prof. David M. Lawson
> Department of Biological Chemistry,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=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/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

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

Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme

On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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