Re: Error in setting up model free analysis

2017-02-21 Thread Edward d'Auvergne
On 21 February 2017 at 07:29, Ashish Sethi  wrote:
> Thanks Sam.
>
>
>
> I did ignore the error message and run the model free analysis and I got the 
> following errors:
>
>
>
> Traceback (most recent call last):
>   File "/usr/local/relax/gui/analyses/execute.py", line 87, in run
> self.run_analysis()
>   File "/usr/local/relax/gui/analyses/auto_model_free.py", line 808, in 
> run_analysis
> dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, 
> pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, 
> diff_model=self.data.global_models, mf_models=self.data.mf_models, 
> local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, 
> diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, 
> mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, 
> conv_loop=self.data.conv_loop)
>   File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 241, in 
> __init__
> self.execute()
>   File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 604, in 
> execute
> self.interpreter.results.read(file='results', 
> dir=self.results_dir+'local_tm'+sep+'aic')
>   File "/usr/local/relax/prompt/uf_objects.py", line 221, in __call__
> self._backend(*new_args, **uf_kargs)
>   File "/usr/local/relax/generic_fns/results.py", line 96, in read
> ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name())
>   File "/usr/local/relax/data/__init__.py", line 452, in from_xml
> self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version)
>   File "/usr/local/relax/data/pipe_container.py", line 255, in from_xml
> self.structure.from_xml(str_nodes[0], dir=dir, id=parser, 
> file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 296, in 
> from_xml
> self.structural_data.from_xml(model_nodes, id=id, 
> file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 1223, in 
> from_xml
> self[-1].mol.from_xml(mol_nodes, id=id, file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 1441, in 
> from_xml
> self[-1].from_xml(mol_node, file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/internal.py", line 2607, in 
> from_xml
> xml_to_object(mol_node, self, file_version=file_version)
>   File "/usr/local/relax/data/relax_xml.py", line 277, in xml_to_object
> value[i] = packBytesAsPyFloat(ieee_value[i])
>   File "/usr/local/relax/float.py", line 200, in packBytesAsPyFloat
> doubleString=pack('8B',*bytes)
> error: pack expected 8 items for packing (got 571)
>
>
>
> Can anyone suggest what is the problem ?

Hi Ashish,

Such an error message means that the relax results file is corrupted
somehow.  Maybe check that you haven't run out of hard disk space or
that there are no bad sectors on the hard disk.  You could also open
up the results_dir+local_tm/aic/results.bz2 file and see if that file
looks ok.  If there is nothing wrong with your hard disk, could you
open up a bug report at https://gna.org/bugs/?func=additem=relax
and attach the results.bz2 file causing the problem?  If you'd like to
keep your data private, try deleting residues from the XML file until
you only have 1 or 2 left, and use the state.load user function to
make sure that that exact "error: pack expected 8 items for packing
(got 571)" message is still present.

Regards,

Edward

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Re: Error in setting up model free analysis

2017-02-20 Thread Edward d'Auvergne
On 21 February 2017 at 05:40, Ashish Sethi  wrote:
> Dear Edward,
>
>
> Hope this email finds you well !!!
>
>
>
> I am a beginner in the field of protein dynamics and I wish to do a model 
> free analysis for my protein which is about 72 residues (8.5 kDa). I have 
> calculated the standard R1, R2 and NOE (steady state) parameters and also did 
> the reduced spectral density mapping.
>
>
> My question is related to dipolar relaxation settings while setting up the 
> model free analysis, so all my files (R1, R2 and NOE) only have 15N spin 
> information and if I follow the instructions given in the manual and select 
> "@N" and "@H"-- i get an error saying no information available for H spin 
> which is obvious. In this case what am I supposed to select ? Apologies for 
> my naivety.

Hi Ashish,

Welcome to the relax mailing lists!  Note for a model-free analysis
that for over 2 decades now it is expected that you collect data at 2
or more field strengths.  I suggest you have a read of the following
reference to understand why a model-free analysis fails - i.e. you end
up with artificial Rex and nanosecond motions:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494.  (http://dx.doi.org/10.1039/b702202f).

As for the error, this should actually be a RelaxWarning saying that
the H spins are deselected as there is no relaxation data.  If you
have a RelaxError, or any other Python Error, could you copy and paste
that error message?  Otherwise, the RelaxWarning is what you should
expect.

Regards,

Edward

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Re: Error in setting up model free analysis

2017-02-20 Thread Ashish Sethi
Thanks Sam.



I did ignore the error message and run the model free analysis and I got the 
following errors:



Traceback (most recent call last):
  File "/usr/local/relax/gui/analyses/execute.py", line 87, in run
self.run_analysis()
  File "/usr/local/relax/gui/analyses/auto_model_free.py", line 808, in 
run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, 
pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, 
diff_model=self.data.global_models, mf_models=self.data.mf_models, 
local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, 
diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, 
mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, 
conv_loop=self.data.conv_loop)
  File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 241, in 
__init__
self.execute()
  File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 604, in 
execute
self.interpreter.results.read(file='results', 
dir=self.results_dir+'local_tm'+sep+'aic')
  File "/usr/local/relax/prompt/uf_objects.py", line 221, in __call__
self._backend(*new_args, **uf_kargs)
  File "/usr/local/relax/generic_fns/results.py", line 96, in read
ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name())
  File "/usr/local/relax/data/__init__.py", line 452, in from_xml
self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version)
  File "/usr/local/relax/data/pipe_container.py", line 255, in from_xml
self.structure.from_xml(str_nodes[0], dir=dir, id=parser, 
file_version=file_version)
  File "/usr/local/relax/generic_fns/structure/api_base.py", line 296, in 
from_xml
self.structural_data.from_xml(model_nodes, id=id, file_version=file_version)
  File "/usr/local/relax/generic_fns/structure/api_base.py", line 1223, in 
from_xml
self[-1].mol.from_xml(mol_nodes, id=id, file_version=file_version)
  File "/usr/local/relax/generic_fns/structure/api_base.py", line 1441, in 
from_xml
self[-1].from_xml(mol_node, file_version=file_version)
  File "/usr/local/relax/generic_fns/structure/internal.py", line 2607, in 
from_xml
xml_to_object(mol_node, self, file_version=file_version)
  File "/usr/local/relax/data/relax_xml.py", line 277, in xml_to_object
value[i] = packBytesAsPyFloat(ieee_value[i])
  File "/usr/local/relax/float.py", line 200, in packBytesAsPyFloat
doubleString=pack('8B',*bytes)
error: pack expected 8 items for packing (got 571)



Can anyone suggest what is the problem ?



Thanks a lot.



Ashish

____________
From: Mahdi, Sam <sam.mahdi@my.csun.edu>
Sent: Tuesday, February 21, 2017 4:17:08 PM
To: Ashish Sethi
Subject: Re: Error in setting up model free analysis

Hi Ashish,

I am not part of Edwards team, just a normal relax user. The error is simply 
informing you there is no information for hydrogen spins (which there shouldn't 
be), so its fine. It will exclude the hydrogen spin dynamics in its 
computations, so there is nothing to worry about in regards to the error (from 
my experience).

Sincerely,
Sam

On Mon, Feb 20, 2017 at 8:40 PM, Ashish Sethi 
<ashish.se...@unimelb.edu.au<mailto:ashish.se...@unimelb.edu.au>> wrote:
Dear Edward,


Hope this email finds you well !!!



I am a beginner in the field of protein dynamics and I wish to do a model free 
analysis for my protein which is about 72 residues (8.5 kDa). I have calculated 
the standard R1, R2 and NOE (steady state) parameters and also did the reduced 
spectral density mapping.


My question is related to dipolar relaxation settings while setting up the 
model free analysis, so all my files (R1, R2 and NOE) only have 15N spin 
information and if I follow the instructions given in the manual and select 
"@N" and "@H"-- i get an error saying no information available for H spin which 
is obvious. In this case what am I supposed to select ? Apologies for my 
naivety.




Thanks


Ashish
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