Dear Edward
Thanks a lot for the reply..
The hard disk on my desktop is fine and there is plenty of storage space on it.
I have attached the results.bz2 file with this email as I couldn't login to my
account which further didn't allow me to generate a bug report.
Thanks
Ashish
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Today's Topics:
1. Error in setting up model free analysis (Ashish Sethi)
2. Error in setting up model free analysis (Ashish Sethi)
3. Re: Error in setting up model free analysis (Ashish Sethi)
4. Re: Error in setting up model free analysis (Edward d'Auvergne)
5. Re: Error in setting up model free analysis (Edward d'Auvergne)
----------------------------------------------------------------------
Message: 1
Date: Tue, 21 Feb 2017 15:37:28 +1100
From: Ashish Sethi <set...@student.unimelb.edu.au>
To: relax-users@gna.org
Subject: Error in setting up model free analysis
Message-ID:
<CAB-9y=q8N8hSR==2FhOTC5KDjFF=jujvomm8y2g7ysckdfg...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
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
--
*Ashish Sethi*
PhD Candidate
Biochemistry and Molecular Biology
Bio21 Molecular Science and Biotechnology Institute
University of Melbourne (Parkville Campus)
30, Flemington Road, Parkville
Victoria 3010, Australia
Tel: +61 3 8344 2504
Mob: 0451211055
Email: set...@student.unimelb.edu.au
------------------------------
Message: 2
Date: Tue, 21 Feb 2017 04:40:24 +0000
From: Ashish Sethi <ashish.se...@unimelb.edu.au>
To: "relax-users@gna.org" <relax-users@gna.org>
Subject: Error in setting up model free analysis
Message-ID:
<me1pr01mb1427613c85f418f9b0702d61ab...@me1pr01mb1427.ausprd01.prod.outlook.com>
Content-Type: text/plain; charset=WINDOWS-1252
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
------------------------------
Message: 3
Date: Tue, 21 Feb 2017 06:29:47 +0000
From: Ashish Sethi <ashish.se...@unimelb.edu.au>
To: "Mahdi, Sam" <sam.mahdi....@my.csun.edu>, "relax-users@gna.org"
<relax-users@gna.org>
Subject: Re: Error in setting up model free analysis
Message-ID:
<me1pr01mb1427ffd9e2becc8e9a46571cab...@me1pr01mb1427.ausprd01.prod.outlook.com>
Content-Type: text/plain; charset=WINDOWS-1252
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
_______________________________________________
relax (http://www.nmr-relax.com<http://www.nmr-relax.com>)
This is the relax-users mailing list
relax-users@gna.org<mailto:relax-users@gna.org>
To unsubscribe from this list, get a password
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------------------------------
Message: 4
Date: Tue, 21 Feb 2017 08:53:28 +0100
From: "Edward d'Auvergne" <edw...@nmr-relax.com>
To: Ashish Sethi <ashish.se...@unimelb.edu.au>
Cc: "relax-users@gna.org" <relax-users@gna.org>
Subject: Re: Error in setting up model free analysis
Message-ID:
<caed9py8vklw5acyolp4eysktfcbz7m2+cgi8onnmvvmbof3...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On 21 February 2017 at 05:40, Ashish Sethi <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.
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
------------------------------
Message: 5
Date: Tue, 21 Feb 2017 09:00:21 +0100
From: "Edward d'Auvergne" <edw...@nmr-relax.com>
To: Ashish Sethi <ashish.se...@unimelb.edu.au>
Cc: "relax-users@gna.org" <relax-users@gna.org>
Subject: Re: Error in setting up model free analysis
Message-ID:
<CAED9pY9aXXpgpKfJwYGUWKLbZL8yMhTSSXK+9-YXYw=xgnh...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On 21 February 2017 at 07:29, Ashish Sethi <ashish.se...@unimelb.edu.au> 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&group=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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