Re: Display the parameters of disfusion tensor using diff_tensor_pdb.py -- February 04, 2013 - 15:35

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