On Thu, 2006-10-26 at 13:45 +1000, Edward d'Auvergne wrote:
During discussions with James Horne, James helped with a lot of
debugging of relax back in 2004 prior to relax being publicly
released, a few ideas were raised about how to represent the diffusion
tensor superimposed onto the 3D molecular structure. This
representation would significantly help in the comparison of different
diffusion tensors. To compare diffusion tensors, you really need to
compare the eigenvalues (Dx, Dy, and Dz, or Dpar and Dper). However
because the corresponding eigenvectors, the axes of the tensor, may
not be the same between two tensors (they could be 90 degrees out),
you really need to orient the diffusion tensor with respect to the
molecule so that you can compare the correct eigenvalues. I'll send
another post with a quick tutorial on diffusion tensors which may help
if there were parts of this paragraph which didn't make sense.
At minimum you need to have the eigenvector representing the unique
axis of the spheroid tensors superimposed onto the structure in 3D, or
the three eigenvectors (axes) of the ellipsoid. For the spheroids
this could possibly be done by adding two bonded atoms into a PDB
file, one at the center of mass, the other placed in the correct
orientation at a scaled distance away from the center atom. Then you
could use the 'neon' representation for them in Molmol.
Extending on the idea, it could be possible to create a picture of the
diffusion tensors in Molmol. This would look similar to the contours
presented in Tensor. By calculating the center of mass, adding atoms
to a PDB file, connecting them, and then using 'neon' or 'line' in
Molmol, a polygon representation of the tensor could be created.
This, combined with the new model-free analysis protocol encoded in
the 'full_analysis.py' sample script, could be the final nail in
Tensor's coffin ;)
This is a nice idea - I like this feature of Tensor.
In the new PDB file, which by default could be called 'tensor.pdb',
the atoms could all be set to a new residue called 'TNS' (an abbrev.
of tensor). The residue could be setup using the HET, HETNAM, and
FORMUL records, each atom could be represented by a HETATM record,
followed by the TER record, and then all the atoms joined up by CONECT
records. The file could be terminated with the MASTER and END
records. Would anyone know how to get Molmol 2K to recognise the
CONECT records as being bonds???
I've never tried too hard, but generaly found Molmol to be pretty
terrible at dealing with HETATMs and CONECT records. An alternative in
molmol would be to use the addDrawobj and moveDrawobj commands in a
macro to add and position the required lines. This would avoid having to
hack pdb files. I guess a third option would be the addTrajec command.
This adds a polyline connecting corresponding atoms in a series of
molecules (intended for illustrating MD trjectories).
I might try to implement these ideas into the 1.3 development line.
Edward
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Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.