Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Martin Noble 

Hi Stuart,

If the wait til Python3 is the issue, surely we are close to pushing the 
trigger ?
Are we confident that other things (like fortran libraries and ad-hos python 
and shell scripts) are good to go ?

M.

Sent from my iPad

On 18 Nov 2020, at 10:13, Stuart McNicholas  
wrote:


Possibly. But i2 itself cannot be fully international until Python3, since 
sqlite in Python2 does not support unicode. Unless we drop sqlite, of course, 
but there will be other libraries that cause problems.

On Wed, 18 Nov 2020 at 09:44, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:
Thanks Stuart,

Of course, since we ar enow in teh 21st Century, maybe we should make these 
problems go away, if necessaryby dropping those elements of the suite that 
can’t handle international, modeern scientists ?


Sent from my iPad

On 18 Nov 2020, at 09:20, Stuart McNicholas 
mailto:stuart.mcnicho...@york.ac.uk>> wrote:


Yes, Martin, we should. I think we're catching and warning about non-ASCII now. 
I'll check if whitespace is in the check as well, and if not add it.

On Wed, 18 Nov 2020 at 09:12, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:
Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?


Sent from my iPad

On 17 Nov 2020, at 13:13, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
 wrote:



⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another 
common Windows problem - not just spaces either, but anything not ASCII 
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi all

The problem turned out to be that the user had a space in their username. 
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
mailto:kevin.cow...@york.ac.uk>> wrote:
Hi!

I have a student trying to run i2, and a task to import merged data from cif 
which works fine for the other students is failing at the pointless step.

The logfiles are identical up to pointless (apart from the random free-R flag 
assignment), but the problem occurs in pointless. The log file output is as 
follows:


 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
(2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group determination, 
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Stuart McNicholas 
Possibly. But i2 itself cannot be fully international until Python3, since
sqlite in Python2 does not support unicode. Unless we drop sqlite, of
course, but there will be other libraries that cause problems.

On Wed, 18 Nov 2020 at 09:44, Martin Noble 
wrote:

> Thanks Stuart,
>
> Of course, since we ar enow in teh 21st Century, maybe we should make
> these problems go away, if necessaryby dropping those elements of the suite
> that can’t handle international, modeern scientists ?
>
>
> Sent from my iPad
>
> On 18 Nov 2020, at 09:20, Stuart McNicholas 
> wrote:
>
> 
> Yes, Martin, we should. I think we're catching and warning about non-ASCII
> now. I'll check if whitespace is in the check as well, and if not add it.
>
> On Wed, 18 Nov 2020 at 09:12, Martin Noble 
> wrote:
>
>> Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?
>>
>>
>> Sent from my iPad
>>
>> On 17 Nov 2020, at 13:13, Stuart McNicholas <
>> 19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> 
>>
>> ⚠ External sender. Take care when opening links or attachments. Do not
>> provide your login details.
>> Dear Kevin,
>>Glad you worked it out. Sorry I missed earlier messages. This is
>> another common Windows problem - not just spaces either, but anything not
>> ASCII alphanumeric is likely to cause problems.
>>
>> Stuart
>>
>> On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan <
>> 2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Hi all
>>>
>>> The problem turned out to be that the user had a space in their
>>> username. Creating a new account solved it.
>>>
>>> Regards,
>>>
>>> On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
>>> wrote:
>>>
 Hi!

 I have a student trying to run i2, and a task to import merged data
 from cif which works fine for the other students is failing at the
 pointless step.

 The logfiles are identical up to pointless (apart from the random
 free-R flag assignment), but the problem occurs in pointless. The log file
 output is as follows:

  Input command lines 


 # Task 4.3.1 pointless running pointless

 # Mini-MTZ input to HKLIN:

 #   Data type   parameter  jobannotation

 NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

 HKLIN 
 C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

 HKLOUT 
 C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

 choose spacegroup P 61


  End of input



 **

 **

 * POINTLESS  *

 *   1.12.2   *

 **

 *   Determine Laue group from unmerged intensities   *

 * Phil Evans MRC LMB, Cambridge  *

 * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

 **

 **



  ERROR 


 $TEXT:Reference: $$ Please cite $$

 P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 
 72-82  (2006).

 http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

 PDF

 P.R.Evans, 'An introduction to data reduction: space-group determination, 
 scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

 http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

 PDF

 $$



 --
 Professor Kevin Cowtan
 Email:  kevin.cow...@york.ac.uk
 Pronouns:   Please use he/him or they/them when referring to me in
 professional contexts
 Address:York Structural Biology Laboratory, Department of Chemistry
 University of York, York, YO10 5DD, UK
 ORCiD:  -0002-0189-1437 
 Web:
 https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
 Disclaimer: http://w 
 ww.york.ac.uk/docs/disclaimer/email.htm
 

>>>
>>>
>>> --
>>> Professor Kevin Cowtan
>>> Email:  kevin.cow...@york.ac.uk
>>> Pronouns:   Please use he/him or they/them when referring to me in
>>> professional contexts
>>> Address:York Structural Biology Laboratory, Department of Chemistry
>>> University of York, York, YO10 5DD, UK
>>> ORCiD:  -0002-0189-1437 
>>> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
>>> Disclaimer: http://w

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Martin Noble 
Thanks Stuart,

Of course, since we ar enow in teh 21st Century, maybe we should make these 
problems go away, if necessaryby dropping those elements of the suite that 
can’t handle international, modeern scientists ?


Sent from my iPad

On 18 Nov 2020, at 09:20, Stuart McNicholas  
wrote:


Yes, Martin, we should. I think we're catching and warning about non-ASCII now. 
I'll check if whitespace is in the check as well, and if not add it.

On Wed, 18 Nov 2020 at 09:12, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:
Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?


Sent from my iPad

On 17 Nov 2020, at 13:13, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
 wrote:



⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another 
common Windows problem - not just spaces either, but anything not ASCII 
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi all

The problem turned out to be that the user had a space in their username. 
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
mailto:kevin.cow...@york.ac.uk>> wrote:
Hi!

I have a student trying to run i2, and a task to import merged data from cif 
which works fine for the other students is failing at the pointless step.

The logfiles are identical up to pointless (apart from the random free-R flag 
assignment), but the problem occurs in pointless. The log file output is as 
follows:


 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
(2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group determination, 
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm



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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Stuart McNicholas 
Yes, Martin, we should. I think we're catching and warning about non-ASCII
now. I'll check if whitespace is in the check as well, and if not add it.

On Wed, 18 Nov 2020 at 09:12, Martin Noble 
wrote:

> Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?
>
>
> Sent from my iPad
>
> On 17 Nov 2020, at 13:13, Stuart McNicholas <
> 19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> 
>
> ⚠ External sender. Take care when opening links or attachments. Do not
> provide your login details.
> Dear Kevin,
>Glad you worked it out. Sorry I missed earlier messages. This is
> another common Windows problem - not just spaces either, but anything not
> ASCII alphanumeric is likely to cause problems.
>
> Stuart
>
> On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan <
> 2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi all
>>
>> The problem turned out to be that the user had a space in their username.
>> Creating a new account solved it.
>>
>> Regards,
>>
>> On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
>> wrote:
>>
>>> Hi!
>>>
>>> I have a student trying to run i2, and a task to import merged data from
>>> cif which works fine for the other students is failing at the pointless
>>> step.
>>>
>>> The logfiles are identical up to pointless (apart from the random free-R
>>> flag assignment), but the problem occurs in pointless. The log file output
>>> is as follows:
>>>
>>>  Input command lines 
>>>
>>>
>>> # Task 4.3.1 pointless running pointless
>>>
>>> # Mini-MTZ input to HKLIN:
>>>
>>> #   Data type   parameter  jobannotation
>>>
>>> NAME PROJECT 2b463 CRYSTAL xtal DATASET dest
>>>
>>> HKLIN 
>>> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz
>>>
>>> HKLOUT 
>>> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz
>>>
>>> choose spacegroup P 61
>>>
>>>
>>>  End of input
>>>
>>>
>>>
>>> **
>>>
>>> **
>>>
>>> * POINTLESS  *
>>>
>>> *   1.12.2   *
>>>
>>> **
>>>
>>> *   Determine Laue group from unmerged intensities   *
>>>
>>> * Phil Evans MRC LMB, Cambridge  *
>>>
>>> * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
>>>
>>> **
>>>
>>> **
>>>
>>>
>>>
>>>  ERROR 
>>>
>>>
>>> $TEXT:Reference: $$ Please cite $$
>>>
>>> P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82 
>>>  (2006).
>>>
>>> http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>
>>>
>>> PDF
>>>
>>> P.R.Evans, 'An introduction to data reduction: space-group determination, 
>>> scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)
>>>
>>> http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>
>>>
>>> PDF
>>>
>>> $$
>>>
>>>
>>>
>>> --
>>> Professor Kevin Cowtan
>>> Email:  kevin.cow...@york.ac.uk
>>> Pronouns:   Please use he/him or they/them when referring to me in
>>> professional contexts
>>> Address:York Structural Biology Laboratory, Department of Chemistry
>>> University of York, York, YO10 5DD, UK
>>> ORCiD:  -0002-0189-1437 
>>> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
>>> Disclaimer: http://w 
>>> ww.york.ac.uk/docs/disclaimer/email.htm
>>> 
>>>
>>
>>
>> --
>> Professor Kevin Cowtan
>> Email:  kevin.cow...@york.ac.uk
>> Pronouns:   Please use he/him or they/them when referring to me in
>> professional contexts
>> Address:York Structural Biology Laboratory, Department of Chemistry
>> University of York, York, YO10 5DD, UK
>> ORCiD:  -0002-0189-1437 
>> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
>> Disclaimer: http://w 
>> ww.york.ac.uk/docs/disclaimer/email.htm
>> 
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Martin Noble 
Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?


Sent from my iPad

On 17 Nov 2020, at 13:13, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:



⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another 
common Windows problem - not just spaces either, but anything not ASCII 
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi all

The problem turned out to be that the user had a space in their username. 
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
mailto:kevin.cow...@york.ac.uk>> wrote:
Hi!

I have a student trying to run i2, and a task to import merged data from cif 
which works fine for the other students is failing at the pointless step.

The logfiles are identical up to pointless (apart from the random free-R flag 
assignment), but the problem occurs in pointless. The log file output is as 
follows:


 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
(2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group determination, 
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm



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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-17 Thread Stuart McNicholas 
Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another
common Windows problem - not just spaces either, but anything not ASCII
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan <
2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi all
>
> The problem turned out to be that the user had a space in their username.
> Creating a new account solved it.
>
> Regards,
>
> On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
> wrote:
>
>> Hi!
>>
>> I have a student trying to run i2, and a task to import merged data from
>> cif which works fine for the other students is failing at the pointless
>> step.
>>
>> The logfiles are identical up to pointless (apart from the random free-R
>> flag assignment), but the problem occurs in pointless. The log file output
>> is as follows:
>>
>>  Input command lines 
>>
>>
>> # Task 4.3.1 pointless running pointless
>>
>> # Mini-MTZ input to HKLIN:
>>
>> #   Data type   parameter  jobannotation
>>
>> NAME PROJECT 2b463 CRYSTAL xtal DATASET dest
>>
>> HKLIN 
>> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz
>>
>> HKLOUT 
>> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz
>>
>> choose spacegroup P 61
>>
>>
>>  End of input
>>
>>
>>
>> **
>>
>> **
>>
>> * POINTLESS  *
>>
>> *   1.12.2   *
>>
>> **
>>
>> *   Determine Laue group from unmerged intensities   *
>>
>> * Phil Evans MRC LMB, Cambridge  *
>>
>> * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
>>
>> **
>>
>> **
>>
>>
>>
>>  ERROR 
>>
>>
>> $TEXT:Reference: $$ Please cite $$
>>
>> P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
>> (2006).
>>
>> http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>
>>
>> PDF
>>
>> P.R.Evans, 'An introduction to data reduction: space-group determination, 
>> scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)
>>
>> http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>
>>
>> PDF
>>
>> $$
>>
>>
>>
>> --
>> Professor Kevin Cowtan
>> Email:  kevin.cow...@york.ac.uk
>> Pronouns:   Please use he/him or they/them when referring to me in
>> professional contexts
>> Address:York Structural Biology Laboratory, Department of Chemistry
>> University of York, York, YO10 5DD, UK
>> ORCiD:  -0002-0189-1437 
>> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
>> Disclaimer: http://w 
>> ww.york.ac.uk/docs/disclaimer/email.htm
>> 
>>
>
>
> --
> Professor Kevin Cowtan
> Email:  kevin.cow...@york.ac.uk
> Pronouns:   Please use he/him or they/them when referring to me in
> professional contexts
> Address:York Structural Biology Laboratory, Department of Chemistry
> University of York, York, YO10 5DD, UK
> ORCiD:  -0002-0189-1437 
> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
> Disclaimer: http://w 
> ww.york.ac.uk/docs/disclaimer/email.htm
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-17 Thread Kevin Cowtan 
Hi all

The problem turned out to be that the user had a space in their username.
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan  wrote:

> Hi!
>
> I have a student trying to run i2, and a task to import merged data from
> cif which works fine for the other students is failing at the pointless
> step.
>
> The logfiles are identical up to pointless (apart from the random free-R
> flag assignment), but the problem occurs in pointless. The log file output
> is as follows:
>
>  Input command lines 
>
>
> # Task 4.3.1 pointless running pointless
>
> # Mini-MTZ input to HKLIN:
>
> #   Data type   parameter  jobannotation
>
> NAME PROJECT 2b463 CRYSTAL xtal DATASET dest
>
> HKLIN 
> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz
>
> HKLOUT 
> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz
>
> choose spacegroup P 61
>
>
>  End of input
>
>
>
> **
>
> **
>
> * POINTLESS  *
>
> *   1.12.2   *
>
> **
>
> *   Determine Laue group from unmerged intensities   *
>
> * Phil Evans MRC LMB, Cambridge  *
>
> * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
>
> **
>
> **
>
>
>
>  ERROR 
>
>
> $TEXT:Reference: $$ Please cite $$
>
> P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
> (2006).
>
> http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>
>
> PDF
>
> P.R.Evans, 'An introduction to data reduction: space-group determination, 
> scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)
>
> http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>
>
> PDF
>
> $$
>
>
>
> --
> Professor Kevin Cowtan
> Email:  kevin.cow...@york.ac.uk
> Pronouns:   Please use he/him or they/them when referring to me in
> professional contexts
> Address:York Structural Biology Laboratory, Department of Chemistry
> University of York, York, YO10 5DD, UK
> ORCiD:  -0002-0189-1437 
> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
> Disclaimer: http://w 
> ww.york.ac.uk/docs/disclaimer/email.htm
> 
>


-- 
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in
professional contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437 
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: http://w 
ww.york.ac.uk/docs/disclaimer/email.htm




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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-17 Thread Phil Evans 
That sort of thing works for me

1. Can you try running Pointless from the command line on the same file?

2. Failing that, can you send me the input file to Pointless to see why 
Pointless is failing

Phil

> On 17 Nov 2020, at 10:23, Kevin Cowtan 
> <2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi!
> 
> I have a student trying to run i2, and a task to import merged data from cif 
> which works fine for the other students is failing at the pointless step.
> 
> The logfiles are identical up to pointless (apart from the random free-R flag 
> assignment), but the problem occurs in pointless. The log file output is as 
> follows:
> 
>  Input command lines 
> 
> # Task 4.3.1 pointless running pointless
> # Mini-MTZ input to HKLIN:
> #   Data type   parameter  jobannotation  
>   
> NAME PROJECT 2b463 CRYSTAL xtal DATASET dest
> HKLIN 
> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz
> HKLOUT 
> C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz
> choose spacegroup P 61
> 
>  End of input
> 
> 
> **
> **
> * POINTLESS  *
> *   1.12.2   *
> **
> *   Determine Laue group from unmerged intensities   *
> * Phil Evans MRC LMB, Cambridge  *
> * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
> **
> **
> 
> 
>  ERROR 
> 
> $TEXT:Reference: $$ Please cite $$
> P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
> (2006).
> http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>
> PDF
> P.R.Evans, 'An introduction to data reduction: space-group determination, 
> scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)
> http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>
> PDF
> $$
> 
> 
> -- 
> Professor Kevin Cowtan
> Email:  kevin.cow...@york.ac.uk
> Pronouns:   Please use he/him or they/them when referring to me in 
> professional contexts
> Address:York Structural Biology Laboratory, Department of Chemistry
> University of York, York, YO10 5DD, UK
> ORCiD:  -0002-0189-1437
> Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
> Disclaimer: http://www.york.ac.uk/docs/disclaimer/email.htm
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-17 Thread Stuart McNicholas 
Dear Kevin,
   It sometimes helps (for reasons unknown) to run i2 as an administrator
once on Windows. Having said that, there may well be a pointless bug or
compiler error which only manifests on some CPUs/Windows version, etc. But
I'd try the run as admin idea first, if it's possible. If it's not
possible, then unfortunately my idea is no use.

Best wishes,
Stuart



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[ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-17 Thread Kevin Cowtan 
Hi!

I have a student trying to run i2, and a task to import merged data from
cif which works fine for the other students is failing at the pointless
step.

The logfiles are identical up to pointless (apart from the random free-R
flag assignment), but the problem occurs in pointless. The log file output
is as follows:

 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62,
72-82  (2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group
determination, scaling and intensity statistics' Acta Cryst. D67,
282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$



-- 
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in
professional contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437 
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: http://w 
ww.york.ac.uk/docs/disclaimer/email.htm




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