On Dec 13, 2007 6:43 AM, Edward d'Auvergne <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 > > > > _______________________________________________ > > relax (http://nmr-relax.com) > > > > This is the relax-users mailing list > > [email protected] > > > > 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-users > > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > 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-users > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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-users
