RE: Problem with modsel.py

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

Perfect!
It's already working.
Thanks once again for your help!
Cheers
Tiago P

-----Original Message-----
From: edw...@do... [mailto:edw...@do...] On
Behalf Of Edward d'Auvergne
Sent: terça-feira, 19 de Janeiro de 2010 10:28
To: Tiago Pais
Cc: rel...@do...
Subject: Re: Problem with modsel.py

Hi,

Thanks for the report.  This is related to unicode and has been
encountered before.  See the thread starting with the post by Olivier
Serve (olivier dott serve att gmail dott com) at
https://mail.gna.org/public/relax-users/2009-12/msg00000.html.  The
reason for the 1 Mb limit is to prevent the Gna! open source
infrastructure from collapsing.  Ideally for a bug report, the data
should be minimal.  In the case of relax, data for just a single spin
can be isolated, the bug reproduced on that, and then the single spin
data files and script attached to the report.  Only a few kilobytes of
data is required.  This not only avoids massive strain on the project
infrastructure, but it makes debugging quicker.  Also, could you check
if this works using the code in the repository?  The fix to bug #14872
(https://gna.org/bugs/?14872) should probably solve your issue.  To
get the code, just type:

$ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3

or if this doesn't work:

$ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3

You will need the Subversion program installed to do this.

Cheers,

Edward

2010/1/18 Tiago Pais <tp...@do...>:
> Hi,
> Could not attach the files to the bug report since they were larger than
> 1024kb. Is there another way I can up load them?
> Edward,
> If this is a potential real bug please let me know so that I can send you
> (perhaps directly to your email) the attached files.
> Regards
> Tiago P
>
> -----Original Message-----
> From: Tiago Pais [mailto:tp...@do...]
> Sent: segunda-feira, 18 de Janeiro de 2010 12:45
> To: 'Tiago Pais'; 'Edward d'Auvergne'
> Cc: rel...@do...
> Subject: Problem with modsel.py
>
> Hi,
> But not everything is still well.
> After sucessufully running the mf_multimodel.py with multiple spins, now I
> am having problems with model selection using the modsel.py script.
> I get the following error message:
> " Model-free model of spin '#snPHSinDiffFrame2CHnoHs_mol1:7&:L@7&@CD1'.
> Data pipe            Num_params_(k)       Num_data_sets_(n)    Chi2
> Criterion
> m5                   3                    3                    0.00000
> 6.00000
> m4                   3                    3                    2.21592
> 8.21592
> m1                   1                    3                    9953.65035
> 9955.65035
> m0                   0                    3                  
 146143.15112
> 146143.15112
> m3                   2                    3                    9953.65035
> 9957.65035
> m2                   2                    3                    2.21592
> 6.21592
> m9                   1                    3                  
 146143.15112
> 146145.15112
> The model from the data pipe 'm5' has been selected.
> RelaxError: The selection string u's' is invalid."
>
> Does anyone have an idea what the problem can be?
>
> I'll make a bug report just to save time if it is the case.
> Cheers
> Tiago Pais
>
>
>
>
> -----Original Message-----
> From: rel...@do... [mailto:rel...@do...] On
> Behalf Of Tiago Pais
> Sent: segunda-feira, 18 de Janeiro de 2010 12:38
> To: 'Edward d'Auvergne'
> Cc: rel...@do...
> Subject: RE: Extracting vectors from multiple spins
>
> Hello all,
> Just to tell you that I seem to have solved issue related to multiple
spins
> vector extraction. I have used the following expressions:
>   "# Load spins
>    structure.load_spins(spin_id='@CA', combine_models=False,
ave_pos=False)
>    structure.load_spins(spin_id='@CB1', combine_models=False,
> ave_pos=False)
>
>    # Set the spin name and then load the NH vectors.
>    spin.name(spin_id='@CA', name='CA')
>    structure.vectors(spin_id='@CA', attached='H*', ave=False)
>    spin.name(spin_id='@CB1', name='CB1')
>    structure.vectors(spin_id='@CB1', attached='H*', ave=False)
>    ....."
>
> I get information that the spins are all extracted and get S2 values for
all
> of them.
> Cheers
> TiagoP
>
>
>
> -----Original Message-----
> From: edw...@do... [mailto:edw...@do...] On
> Behalf Of Edward d'Auvergne
> Sent: quarta-feira, 6 de Janeiro de 2010 16:42
> To: Tiago Pais
> Cc: rel...@do...
> Subject: Re: Extracting vectors from multiple spins
>
> Hi,
>
> If you load the PDB file, you need to then need to execute
> structure.load_spins() for 'CA' and 'CB' separately.  Not all atoms of
> the PDB file are treated as spin systems, you must manually specify
> these.  There should be in the save file spin containers, i.e. XML
> elements starting and ending with spin desc="Spin container" name="CA"
> num="???"> and </spin> respectively.  Only then will you be able to
> say that protons are attached to these spins.
>
> Regards,
>
> Edward
>
>
> 2010/1/6 Tiago Pais <tp...@do...>:
>> Well, the spins of interest are also present in the pdb file previously
>> loaded.
>>
>> -----Original Message-----
>> From: edw...@do... [mailto:edw...@do...] On
>> Behalf Of Edward d'Auvergne
>> Sent: quarta-feira, 6 de Janeiro de 2010 16:17
>> To: Tiago Pais
>> Cc: rel...@do...
>> Subject: Re: Extracting vectors from multiple spins
>>
>> Hi,
>>
>> This is strange, it should work!  Could you file a bug report for
>> this?  If you include data for one or two spins that can reproduce
>> this, and the script that was used, I should be able to sort out what
>> is happening very quickly.  Though maybe it's just in the script.  If
>> you have the 'CA' and 'CB' spins loaded, the structure.vectors() call
>> should work.  Are these spins loaded into the program before calling
>> structure.vectors()?
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> 2010/1/4 Tiago Pais <tp...@do...>:
>>> I have tried that before but it doesn't work - there's the spin.name
>> issue.
>>> When it is running the second spin there is a warning message:
>>>>RelaxWarning: The spin ':140&:W@CD1' is already named.  Set the force
> flag
>>> to rename
>>> It goes like this for all the residues and then it stops:
>>>>The attached atom is not a proton.
>>>>
>>>>RelaxError: No vectors could be extracted.
>>>
>>> Cheers
>>> TiagoP
>>>
>>>
>>> -----Original Message-----
>>> From: Edward d'Auvergne [mailto:edw...@do...]
>>> Sent: segunda-feira, 4 de Janeiro de 2010 10:46
>>> To: Tiago Pais
>>> Cc: rel...@do...
>>> Subject: Re: Extracting vectors from multiple spins
>>>
>>> Hi,
>>>
>>> You could try something such as:
>>>
>>> relax> structure.vectors(spin_id='@CA', attached='H1', ave=False)
>>>
>>> and:
>>>
>>> relax> structure.vectors(spin_id='@CB', attached='H2', ave=False)
>>>
>>> if that is how the atoms are named.  Hope this helps.
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>>
>>> 2009/12/17 Tiago Pais <tp...@do...>:
>>>> Hello guys,
>>>>
>>>> Does anyone know if it is possible to extract vectors for multiple
spins
>>> in
>>>> the same run?
>>>>
>>>> Lets say I would like to extract vectors for example from Ca to H1 and
> Cb
>>> to
>>>> H2. For the proton attached I imagine one can use the * character but
>>> for
>>>> the spin itself I dont see how it can be done.
>>>>
>>>> If anyone has any idea, please reply.
>>>>
>>>> Cheers
>>>>
>>>> Tiago P
>>>>
>>>>
>>>>
>>>> **************************************
>>>>
>>>> Tiago Pais, PhD. student
>>>>
>>>> Cell Physiology & NMR
>>>>
>>>> Instituto de Tecnologia Química e Biológica-Oeiras
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
>>>> This is the relax-users mailing list
>>>> rel...@do...
>>>>
>>>> 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
>>>>
>>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
>> This is the relax-users mailing list
>> rel...@do...
>>
>> 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
>>
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-users mailing list
> rel...@do...
>
> 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
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-users mailing list
> rel...@do...
>
> 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
>

RE: Problem with modsel.py

Molecular dynamics by NMR data analysis

RE: Problem with modsel.py