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, <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> 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
Re: relax-users Digest, Vol 78, Issue 5