Re: Display the parameters of disfusion tensor using diff_tensor_pdb.py -- February 04, 2013 - 17:21

Hi Edward,

Thank you very much for your answers and your patience. I will read  
this files carefully. Thank you.

Regards,

Mengjun



Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

> The number of 2304 is based the mathematics of Euler angles together
> with the symmetries in the diffusion tensor space (as I described at
> http://article.gmane.org/gmane.science.nmr.relax.user/1383 with the 12
> axis order combinations, 2 frames of reference - fixed or rotated, 2
> rotational directions - forwards and reverse, 2 handednesses, 6
> eigenvalue orderings, and 4 rotational symmetries).  More information
> about these different conventions can be found at
> http://en.wikipedia.org/wiki/Euler_angles together with my paper:
>
> d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
> dynamic models I. Minimisation algorithms and their performance within
> the model-free and Brownian rotational diffusion spaces. J. Biomol.
> NMR, 40(2), 107-119. (http://dx.doi.org/10.1007/s10858-007-9214-2)
>
> See for example figure S24 of the supplement for the ellipsoid
> diffusion tensor symmetries
> (http://link.springer.com/content/esm/art:10.1007/s10858-007-9214-2/MediaObjects/10858_2007_9214_MOESM1_ESM.pdf).
>
> Regards,
>
> Edward
>
>
> On 4 February 2013 15:34,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > Hi Edward,
> >
> > Thank you very much for your suggestions, I will read them and the
> > suggestions at http://article.gmane.org/gmane.science.nmr.relax.user/1383
> > more carefully. By the way, the number 2304 (Euler angle combinations)
> > depends on the pdb file used? Thank you.
> >
> > Regards,
> >
> > Mengjun
> >
> >
> >
> > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> >
> > > Hi Mengjun,
> > >
> > > Please see below:
> > >
> > >
> > > > I would like to ask you how to display the parameters of disfusion tensor
> > > > calculated from hydronmr in a pdb file.
> > >
> > >
> > > Firstly, note that you will need to know the format of the parameters
> > > from hydronmr.  There are 2304 Euler angle combinations and you need
> > > to match the exact 1 with relax to read the parameters correctly!  I
> > > mentioned this before at:
> > >
> > > http://article.gmane.org/gmane.science.nmr.relax.user/1383
> > >
> > > Converting to the correct convention is incredibly important and relax
> > > will not do that for you.  Otherwise your tensor will be rotated
> > > almost randomly in space!
> > >
> > >
> > > > I understand that diff_tensor_pdb.py
> > > > can do this.
> > >
> > >
> > > This will create a PDB representation of the diffusion tensor and then
> > > display it in PyMOL.
> > >
> > >
> > > > I understand that results.read(file='results.bz2', dir=None)
> > > > can read the parameters of tensor optimized in Relax,
> > > > results.read(file='results.bz2', dir=None) can read the paramters of
> > > > diffusion tensor from hydronmr?
> > >
> > >
> > > No, the results.read user function is only for relax results files -
> > > see http://www.nmr-relax.com/manual/results_read.html.
> > >
> > >
> > > > I would like to submit fine the parameters of tensor simulated in
> > > > hydronmr,
> > > > and the pdb file, it seems that no files can be submitted under support
> > > > now?
> > >
> > >
> > > You will need to create your own script, and maybe be a bit creative.
> > > You can perform all of this in relax, but you will need to discover
> > > how.  As a hint, have a look at the following documentation for
> > > example:
> > >
> > > http://www.nmr-relax.com/manual/pipe_create.html
> > > http://www.nmr-relax.com/manual/diffusion_tensor_init.html
> > > http://www.nmr-relax.com/manual/diffusion_tensor_display.html
> > > http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html
> > > http://www.nmr-relax.com/manual/pymol_tensor_pdb.html
> > > http://www.nmr-relax.com/manual/molmol_tensor_pdb.html
> > >
> > > I hope this helps.
> > >
> > > Regards,
> > >
> > > Edward