Oh, maybe you want the spin loop set up like:
for spin, spin_id in spin_loop(return_id=True):
print "%s %s" % (spin_id, spin.xh_vect)
So you know which molecule/residue/atom you are looking at.
Regards,
Edward
On Sun, Jan 18, 2009 at 1:26 PM, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
> Hi,
>
> relax already stores all the bond vectors in the spin container, if
> the ave argument to structure.vectors() is set to False and multiple
> models are loaded. There's nothing to dump these values to a file yet
> though (value.write() I don't think can output lists or vectors), or
> nothing to really process these vectors. A script skeleton that could
> access all these vectors though would be something like:
>
> from generic_fns.mol_res_spin import spin_loop
> pipe.create()
> structure.read_pdb()
> structure.vectors()
> for spin in spin_loop():
> print spin.xh_vect
>
> This gives you access to the data you require - you just have to set
> up the arguments correctly and dump the data as you wish.
>
> Regards,
>
> Edward
>
>
> On Sat, Jan 17, 2009 at 10:33 PM, Sébastien Morin
> <sebastien.mori...@ulaval.ca> wrote:
>> Hi Ed,
>>
>> Thanks for the detailed and rapid answer !
>>
>> These functionalities would be great ! The use of X-H vectors
>> orientations spread could be used in cases where several structures are
>> present to assess flexibility from different structures ! This would
>> allow a better use of these structures, but also a better
>> rationalization of NMR dynamics !
>>
>> I propose these ideas could be added in the (already quite long) todo
>> list... ;)
>>
>> As for what will soon be possible within relax, i.e. the possibility for
>> the spin container to be filled with a list of orientations, how would
>> you use relax to extract these orientations and output a list for each
>> spin ? Is there a sample script for doing something like that ? This
>> would be useful for someone interested in getting the orientations and
>> analysing them out of relax, until the code is present... ;)
>>
>> Regards,
>>
>>
>> Séb :)
>>
>>
>>
>>
>> Edward d'Auvergne wrote:
>>> Hi,
>>>
>>> I'm actually changing that code at the moment. If you follow my
>>> commit messages you'll see how this will be handled in relax, very
>>> soon. The changes are happening in the multi_structure branch where I
>>> am introducing the distinction between different models (the same
>>> molecules but with different conformations) verses different molecules
>>> within one model. I'm modifying the structure.vectors() user function
>>> now, and this is probably the one you are interested in. Using this
>>> function, you can extract the vectors from all different models and
>>> these will be placed in the spin container. With the 'ave' arg set to
>>> False, each spin container will have a list of 3D vectors for all
>>> models.
>>>
>>> As for analysing the spread of these vectors and then doing something
>>> with that, nothing is present in relax. If you would like to have
>>> this functionality, a little work will need to be done and a few
>>> algorithms designed. The eliminate() user function for deselecting
>>> spins is close but not quite what you need. It accepts an arbitrary
>>> function but is not the correct place for this idea. Better would be
>>> something like:
>>>
>>> deselect.mobile()
>>> deselect.structural_noise()
>>> deselect.vectors()
>>> deselect.spread_vectors()
>>>
>>> with an argument such as (vector_spread_cutoff=0.53), where 0.53 is
>>> some measure of the spread. This might be expandable to B-factors.
>>> If the name deselect.mobile() is used, this could cover a vector
>>> spread, B-factors, low S2 values, etc. Oh, with the deselect user
>>> functions, there should always be a counterpart in the select user
>>> function class. This will allow the deselected spins of the first
>>> analysis to be used in a second with local tm values rather than a
>>> global diffusion tensor. Is this what you had in mind?
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>> On Thu, Jan 15, 2009 at 4:33 PM, Sébastien Morin
>>> <sebastien.mori...@ulaval.ca> wrote:
>>>
>>>> Hi,
>>>>
>>>> We are currently studying a system for which many structures are available.
>>>>
>>>> We thought it would be a great idea to compare X-H (N-H in our case)
>>>> orientations to spot residues for which the orientation varies in the
>>>> different structures, i.e. for which there might be important motions.
>>>>
>>>> We thought this could be useful to eliminate such residues with
>>>> tremendous motions from diffusion tensor optimization and test them as
>>>> diffusing independently (local tm).
>>>>
>>>> Is there a way to do that in relax ?
>>>>
>>>> We saw the sample script 'xh_vector_dist.py' which allows one to plot
>>>> the vector orientations distribution. However, what we would like to get
>>>> would be a file containing the orientations which could allow us to
>>>> compare different structures quantitatively on a per residue basis...
>>>>
>>>> Thanks for help !
>>>>
>>>>
>>>> Sébastien Morin
>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
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>>>>
>>>>
>>>
>>>
>>
>>
>
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