On 10/16/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi Daniel
Calculations for the reduced spectral density mapping need only the R1, R2
and NOE at one field. R1, R2 and NOE are 3 variables you measure and you
extract 3 parameters from them. This is only a simple calculation using in
relax the equations that follow :
j0 = -1.5 / (3.0*d + c) * (0.5*r1 - r2 + 0.6*sigma_noe)
jwx = 1.0 / (3.0*d + c) * (r1 - 1.4*sigma_noe)
jwh = sigma_noe / (5.0*d)
where j0, jwx and jwh are, respectively, the spectral density at the zero
frequency, at the nitrogen frequency (in the special case where you work
with 15N relaxation) and at the apparent proton frequency (sometimes called
J(wH) or J(0.87wH) ).
The other constants and variables are :
c = CSA constant
d = dipolar constant
sigma_noe = cross-relaxation rate (calculated using NOE and R1)
That said, you can extract spectral densities using data from different
magnetic fields at the same time. This only changes the obtained value for
J(0), as J(wN) and J(wH) are field dependent... For example, if you have
data at three fields, you would get 1 value for J(0), 3 values for J(wN) and
3 values for J(wH). This approach is not yet implemented in relax, but it
could be something useful. In fact, it's something I personally would like
to contribute when I have time, maybe this fall...
This description is exact. There are actually a number of
methodologies available for determining J(0) using multiple field
strength data but I have never had the chance to implement these in
relax. The addition of any new type of analysis to relax would be
almost guaranteed to be accepted though. Daniel, the link that Seb
gave in his post
(https://mail.gna.org/public/relax-users/2006-11/msg00019.html) goes
into much more detail into all of this.
However, calculating J(0) using different fields in separated calculations
is something useful you may want to do prior to any calculation using
multiple field data. The reason is that J(0) should be field independent, in
cases where us-ms motions (Rex in the model-free language) are not present.
Thus, calculating J(0) helps you assess the quality of your data. This is
quite important as different factors may influence the consistency of your
data acquired at different magnetic fields...
A part of relax is specially designed to do 3 different consistency tests :
J(0), Fn and FR2. Those consistency tests are implemented in a special
branch of relax which contains, apart from that, all the same functions. A
sample script is also available as for other functions within relax. You can
get that version of the program with svn by typing :
svn co
http://svn.gna.org/svn/relax/branches/consistency_tests_1.2/
.
This branch is likely to be incorporated into the 1.2 line soonish.
These consistency tests will be quite useful especially prior to
reduced spectral density mapping using data at multiple field
strengths to determine a single J(0) value. Seb, what is the status
of this code? Is it now complete? Or do you thing that more testing
required? I will probably try to release a new version of relax soon,
as this is long overdue, and then hopefully we can get your code in
shape for merging for the next version.
Regards,
Edward
Re: Reduced spectral density mapping at three fields