On Dec 13, 2007 6:43 AM, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:
Hi,
The article you reference is a description of the use of the
'full_analysis.py' script distributed with relax. This script
implements a new model-free protocol which is described in Chapter 6
of my PhD thesis
(http://eprints.infodiv.unimelb.edu.au/archive/00002799/) and which
should be published very, very soon. You can use the diffusion
tensor(s) from the Tensor program in relax but be careful. As the
convention for the spherical and Euler angles used in Tensor are
undocumented I was unable to determine, even after asking, what they
are. In Tensor I don't know how the symmetries are handled and
collapsed, whether 0 degrees for the azimuthal angle and alpha and
gamma is along x or y, whether the polar angle and beta range between
-pi/2 to pi/2 or between 0 and pi, or whether the Euler angles are in
the standard physics z-y-z notation, in the shifted axis system
z-y'-z', z-x-z, or roll-pitch-yaw, etc. These are all nicely
described on Wikipedia.
I had similar issues working out the conventions used by Tensor. The
easy solution is provided by Tensors ability to write a PDB file in
the frame of the current diffusion tensor. If you use that file as
input for relax, you can set all Euler/sperical angles to 0 to recover
the tensor orientation as optimised by Tensor. In my hands this argeed
well with tensors as optimised with relax (conventionally, or with
full_analysis.py), though milage will vary depending on the system and
data quantity/quality.
The point of the new protocol is that the model-free parameters are
determined before the global diffusion tensor. This is in contrast to
the current procedure where you start with the diffusion tensor then
finally find the model-free parameters. Hence the new protocol does
not use the initial tensor estimate from Tensor (this is an estimate
as many assumptions about the internal motions are made and mobile
residues should be filtered out first). Note though that this
protocol minimally requires 4 relaxation data sets and optimally 6,
hence to use it you cannot avoid collecting at multiple field
strengths. I hope this answers you questions.
Regards,
Edward
On Dec 12, 2007 12:51 PM, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi,
In the following post [https://mail.gna.org/public/relax-users/
2007-05/msg00009.html], Edward said that relax could be used to
estimate the diffusion tensor parameters (instead of using the
program Tensor). Does this protocol already exist in the form of a
python script? If not, could someone briefly outline the protocol in
an email so I can write it myself?
Thanks,
Doug
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Re: initial estimate of the diffusion tensor