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
Re: Display the parameters of disfusion tensor using diff_tensor_pdb.py