Re: Error in model free analysis

[Edward d'Auvergne]

Hi Ashish,

I had a look at the results file, and I think the problem is that you
are loading a corrupted PDB file format.  The Z coordinates for all
atoms is set to None!  You can see this at the bottom of the file.
The first few coordinates are:


[-14.56, -14.35, -12.87, -12.01, -14.73, -16.17, ...
[snip]


[6.0, 2.0, 9.0, 1.0, 5.0, 7.0, ...
[snip]


[None, None, None, None, None, None, ...


Because of the strange coordinates, especially integers for the Y
coordinate and nothing for the Z, this can only be an incorrectly
formatted PDB file.  Note that the character position is what counts
in the PDB format.  Could this be the reason?

Regards,

Edward



On 22 February 2017 at 12:01, Ashish Sethi <ashish.se...@unimelb.edu.au> wrote:
> Hi Troels,
>
>
>
> I am having troubles login to my account. So I have uploaded the results.bz2 
> file on my drop box and this is the link to it:
>
>
> https://www.dropbox.com/s/86teapt1isbo8zr/results.bz2?dl=0
>
>
>
> Hope this helps to access the files.
>
>
> Thanks
>
>
> Ashish
>
> 
> From: tlin...@gmail.com <tlin...@gmail.com> on behalf of Troels Emtekær 
> Linnet <tlin...@nmr-relax.com>
> Sent: Wednesday, February 22, 2017 8:02:24 PM
> To: Ashish Sethi
> Cc: relax-users@gna.org
> Subject: Re: Error in model free analysis
>
> Hi Ashish.
>
> Attachments to the mailserver is dropped.
> Can you provide a bug report instead, at upload the file there?
>
> https://gna.org/bugs/?func=additem=relax<https://gna.org/bugs/?func=additem=relax>
>
> Best
> Troels
>
> 2017-02-22 8:56 GMT+01:00 Ashish Sethi 
> <ashish.se...@unimelb.edu.au<mailto:ashish.se...@unimelb.edu.au>>:
> Dear Edward,
>
>
>
> I also tried running the same calculation on my personal macbook pro (OSx EI 
> Capitan) and I got the following errors:
>
>
> relax> results.read(file='results', dir='/Users/ashishsethi/Desktop/model 
> free LDLamodule/local_tm/aic')
>
> Opening the file '/Users/ashishsethi/Desktop/model free 
> LDLamodule/local_tm/aic/results.bz2' for reading.
>
> Exception raised in thread.
>
>
> Traceback (most recent call last):
>
>   File "gui/analyses/execute.pyc", line 87, in run
>
>   File "gui/analyses/auto_model_free.pyc", line 811, in run_analysis
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 246, in __init__
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 652, in execute
>
>   File "prompt/uf_objects.pyc", line 225, in __call__
>
>   File "pipe_control/results.pyc", line 97, in read
>
>   File "data_store/__init__.pyc", line 512, in from_xml
>
>   File "data_store/pipe_container.pyc", line 244, in from_xml
>
>   File "lib/structure/internal/object.pyc", line 1714, in from_xml
>
>   File "lib/structure/internal/models.pyc", line 155, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 632, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 449, in from_xml
>
>   File "lib/xml.pyc", line 287, in xml_to_object
>
>   File "lib/float.pyc", line 200, in packBytesAsPyFloat
>
> error: pack expected 8 items for packing (got 571)
>
>
>
> I have attached the results.bz2 file with this email.
>
>
>
> Thanks
>
>
> Ashish
> ___
> relax (http://www.nmr-relax.com<http://www.nmr-relax.com>)
>
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Re: Error in model free analysis

[Ashish Sethi]

Hi Troels,



I am having troubles login to my account. So I have uploaded the results.bz2 
file on my drop box and this is the link to it:


https://www.dropbox.com/s/86teapt1isbo8zr/results.bz2?dl=0



Hope this helps to access the files.


Thanks


Ashish


From: tlin...@gmail.com <tlin...@gmail.com> on behalf of Troels Emtekær Linnet 
<tlin...@nmr-relax.com>
Sent: Wednesday, February 22, 2017 8:02:24 PM
To: Ashish Sethi
Cc: relax-users@gna.org
Subject: Re: Error in model free analysis

Hi Ashish.

Attachments to the mailserver is dropped.
Can you provide a bug report instead, at upload the file there?

https://gna.org/bugs/?func=additem=relax<https://gna.org/bugs/?func=additem=relax>

Best
Troels

2017-02-22 8:56 GMT+01:00 Ashish Sethi 
<ashish.se...@unimelb.edu.au<mailto:ashish.se...@unimelb.edu.au>>:
Dear Edward,



I also tried running the same calculation on my personal macbook pro (OSx EI 
Capitan) and I got the following errors:


relax> results.read(file='results', dir='/Users/ashishsethi/Desktop/model free 
LDLamodule/local_tm/aic')

Opening the file '/Users/ashishsethi/Desktop/model free 
LDLamodule/local_tm/aic/results.bz2' for reading.

Exception raised in thread.


Traceback (most recent call last):

  File "gui/analyses/execute.pyc", line 87, in run

  File "gui/analyses/auto_model_free.pyc", line 811, in run_analysis

  File "auto_analyses/dauvergne_protocol.pyc", line 246, in __init__

  File "auto_analyses/dauvergne_protocol.pyc", line 652, in execute

  File "prompt/uf_objects.pyc", line 225, in __call__

  File "pipe_control/results.pyc", line 97, in read

  File "data_store/__init__.pyc", line 512, in from_xml

  File "data_store/pipe_container.pyc", line 244, in from_xml

  File "lib/structure/internal/object.pyc", line 1714, in from_xml

  File "lib/structure/internal/models.pyc", line 155, in from_xml

  File "lib/structure/internal/molecules.pyc", line 632, in from_xml

  File "lib/structure/internal/molecules.pyc", line 449, in from_xml

  File "lib/xml.pyc", line 287, in xml_to_object

  File "lib/float.pyc", line 200, in packBytesAsPyFloat

error: pack expected 8 items for packing (got 571)



I have attached the results.bz2 file with this email.



Thanks


Ashish
___
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Re: Error in model free analysis

[Troels Emtekær Linnet]

Hi Ashish.

Attachments to the mailserver is dropped.
Can you provide a bug report instead, at upload the file there?

https://gna.org/bugs/?func=additem=relax

Best
Troels

2017-02-22 8:56 GMT+01:00 Ashish Sethi :

> Dear Edward,
>
>
>
> I also tried running the same calculation on my personal macbook pro (OSx
> EI Capitan) and I got the following errors:
>
>
> relax> results.read(file='results', dir='/Users/ashishsethi/Desktop/model
> free LDLamodule/local_tm/aic')
>
> Opening the file '/Users/ashishsethi/Desktop/model free
> LDLamodule/local_tm/aic/results.bz2' for reading.
>
> Exception raised in thread.
>
>
> Traceback (most recent call last):
>
>   File "gui/analyses/execute.pyc", line 87, in run
>
>   File "gui/analyses/auto_model_free.pyc", line 811, in run_analysis
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 246, in __init__
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 652, in execute
>
>   File "prompt/uf_objects.pyc", line 225, in __call__
>
>   File "pipe_control/results.pyc", line 97, in read
>
>   File "data_store/__init__.pyc", line 512, in from_xml
>
>   File "data_store/pipe_container.pyc", line 244, in from_xml
>
>   File "lib/structure/internal/object.pyc", line 1714, in from_xml
>
>   File "lib/structure/internal/models.pyc", line 155, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 632, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 449, in from_xml
>
>   File "lib/xml.pyc", line 287, in xml_to_object
>
>   File "lib/float.pyc", line 200, in packBytesAsPyFloat
>
> error: pack expected 8 items for packing (got 571)
>
>
>
> I have attached the results.bz2 file with this email.
>
>
>
> Thanks
>
>
> Ashish
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users
>
___
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Error in model free analysis

[Ashish Sethi]

Dear Edward,



I also tried running the same calculation on my personal macbook pro (OSx EI 
Capitan) and I got the following errors:


relax> results.read(file='results', dir='/Users/ashishsethi/Desktop/model free 
LDLamodule/local_tm/aic')

Opening the file '/Users/ashishsethi/Desktop/model free 
LDLamodule/local_tm/aic/results.bz2' for reading.

Exception raised in thread.


Traceback (most recent call last):

  File "gui/analyses/execute.pyc", line 87, in run

  File "gui/analyses/auto_model_free.pyc", line 811, in run_analysis

  File "auto_analyses/dauvergne_protocol.pyc", line 246, in __init__

  File "auto_analyses/dauvergne_protocol.pyc", line 652, in execute

  File "prompt/uf_objects.pyc", line 225, in __call__

  File "pipe_control/results.pyc", line 97, in read

  File "data_store/__init__.pyc", line 512, in from_xml

  File "data_store/pipe_container.pyc", line 244, in from_xml

  File "lib/structure/internal/object.pyc", line 1714, in from_xml

  File "lib/structure/internal/models.pyc", line 155, in from_xml

  File "lib/structure/internal/molecules.pyc", line 632, in from_xml

  File "lib/structure/internal/molecules.pyc", line 449, in from_xml

  File "lib/xml.pyc", line 287, in xml_to_object

  File "lib/float.pyc", line 200, in packBytesAsPyFloat

error: pack expected 8 items for packing (got 571)



I have attached the results.bz2 file with this email.



Thanks


Ashish
___
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