I forgot to mention, but my 2007 paper also describes a lot of the issues you will encounter. It also will give you citations to all of the relevant literature. See http://www.nmr-relax.com/refs.html#dAuvergneGooley07.
Regards, Edward On 14 January 2013 09:50, Edward d'Auvergne <[email protected]> wrote: > Hi Mengjun, > > For the initial diffusion tensor estimate, you can use Rotdif, > hydronmr, etc., but the only problem is that each of these programs > uses a different angular convention, often without clearly stating > which is used. For example with Euler angles, there are 2304 > different combinations (12 axis order combinations, 2 frames of > reference - fixed or rotated, 2 rotational directions - forwards and > reverse, 4 rotational symmetries, 2 handednesses, and 6 eigenvalue > orderings). You will need to know all of this information for one set > of Euler angles to convert it and use it in another. There are less > combinations for the spheroid tensors, but there are still severe > conversion problems > (http://thread.gmane.org/gmane.science.nmr.relax.user/464/focus=465). > These angular convention conversions must be done by hand. > > If you have a look at the relax mailing lists, you will see that this > has been extensively discussed before. You can search the mailing > lists using the relax website: > > http://www.nmr-relax.com/communication.html#mailing_list_search > > Or you can search in one of the permanent mailing list archives: > > Gmane: http://dir.gmane.org/gmane.science.nmr.relax.user > Mail-archive: http://www.mail-archive.com/relax-users%40gna.org > MARC: http://marc.info/?l=relax-users > > I have found a few in the Gmane archive for you to read through. > These are threads, so it would be useful to read some of the messages > before and after these (which you can see at the top of these links): > > http://thread.gmane.org/gmane.science.nmr.relax.user/1152/focus=1153 > http://thread.gmane.org/gmane.science.nmr.relax.user/1086/focus=1087 > http://thread.gmane.org/gmane.science.nmr.relax.user/968/focus=969 > http://thread.gmane.org/gmane.science.nmr.relax.user/885/focus=891 > http://thread.gmane.org/gmane.science.nmr.relax.user/836/focus=856 > http://thread.gmane.org/gmane.science.nmr.relax.user/464/focus=465 > http://thread.gmane.org/gmane.science.nmr.relax.user/315/focus=340 > http://thread.gmane.org/gmane.science.nmr.relax.user/288/focus=313 > http://thread.gmane.org/gmane.science.nmr.relax.user/276/focus=285 > http://thread.gmane.org/gmane.science.nmr.relax.user/206/focus=208 > > Although there is a lot of reading here, note that each of these > threads contains information relevant for your analysis (some less > than others). Once you have read these in full, you should be able to > find the reference to the section of my PhD thesis > (http://eprints.infodiv.unimelb.edu.au/archive/00002799/ and > http://www.amazon.com/Protein-Dynamics-Model-free-Analysis-Relaxation/dp/3639057627) > that you will need. I'll let you find it yourself as you should learn > a lot when reading the information in these threads. Note that I made > a mistake in one of the messages and mentioned model m0. Once you are > up to speed with all of this, you should see that I meant model m1. > If this is not clear, it is a sign that you have not read enough ;) > > Good luck, > > Edward > > > > > > On 14 January 2013 01:06, <[email protected]> wrote: >> Dear Dr. Edward d'Auvergne, >> >> I am sorry about that. I will not add files to mailing list messages in the >> future. I will use http://gna.org/projects/relax to add files. >> >> Thank you so much for your detailed answers. There are many calculations in >> a complete model free analysis. >> >> About the estimation of the initial diffusion tensor, which can be >> calculated in Rotdif, protein dynamics center, or hydronmr etc., I >> understand that the initial diffusion tensor can be also calculated in >> Relax, I do not know how to do it till now, I just use the >> diffusion_tensor.init(1e-8, fixed=True) in mf_multimodel.py. I would like to >> ask you how to calculate the initial diffusion tensor in Relax? >> >> Thank you very much. >> >> With best regards, >> >> Mengjun Xue _______________________________________________ relax (http://www.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
