On Sat, 2006-11-11 at 14:52 +1100, Edward d'Auvergne wrote:
Now that I've finished writing the code in the 'tensor_pdb' branch,
I'll soon merge it back into the 1.3 line. Chris, the work on the
scaling of the diffusion rates to be proportional to mass in the
tensor PDB file can continue within the 1.3 line. Anyway, if you make
any changes to the 'tensor_pdb' branch after the merge, don't worry,
it's easy enough to port those changes back into the 1.3 line.
Oh, do you think it should be inversely proportional so that the
bigger the molecule, the bigger the tensor? In a hybrid model created
using run.hybridise(), do you think we should scale the multiple
diffusion tensors equally? One way would be to loop over every last
atom in the PDB and get the mass of the entire lot (rather than just
the selected residues).
I was going to suggest this in all cases. The diffusion tensor applies
to and is determined by all atoms in the molecule, not just the ones we
happen to be analysing in any particular run. Thus the mass, center of
mass, and molecular dimentions for scaling should be calculated for all
atoms in the PDB
In any case, the diffusion rate per Angstrom should be made abundantly
clear to the user so that they then hopefully report the rate per
Angstrom in their figure legend. I personally feel that this is
essential, despite the fact Tensor hides this info. It's not uncommon
in the literature for the diffusion tensor parameters to not be
reported. Comparisons are very important, especially if working on a
homologous system, attempting to replicate published results, or
reanalysing data.
I agree that reporting the diffusion tensor is critical in relaxation
analysis. I would go further and say a figure of this type, even if the
scale is reported, is not an alternative to reporting actual values for
the tensor components. Even with a scale, this figure gives no truely
quantitative data, in part it is a two dimentional projection of a 3D
object, and also because the degree of magnification is never reported
in this type of cartoon structural figure ie. even with a scale an a
ruler, I can never work out the size of the diffusion tensor from this
figure. For this reason I'm not so hung up about the scale, but ofcourse
it needs to be clearly reported by relax and perhaps written as a REMARK
to the pdb file.
Chris
An ideal way of doing this could be as follows. Add an atom to the
positive pole of the vector distribution, probably about 5-10
Angstroms out from the pole. Give it a unique atom name for selection
and add it to a new residue named something like RT for the diffusion
rate. The HETNAM record could then contain the string "Diffusion rate
per Angstrom: " + `1.0 / scale` in the chemical name field. Finally
the 'pymol.tensor_pdb()' function displays the chemical name for that
residue. This way, the significance of the magnitude of the tensor is
unavoidable. The labelling can always be turned off in PyMOL, but
this way the user is confronted with this useful info.
Cheers,
Edward
P.S. Once merged, I'll rename the 'pdb' user function class to 'structure'.
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel
Re: Merging of the 'tensor_pdb' branch back into the 1.3 line, autoscaling of the tensor PDB, and the diffusion rate per Angstrom.