Hi !
I've checked the equations used for reduced spectral density mapping in
relax. They're all right... The assumption about the factor of (mu0 /
(4pi))^2 is ok since the old equations were written in Gaussian units
(cgs) and now we use SI units.
However, 2 things seem to be wrong.
1.
The frequencies need not to be scaled by a factor of 2 pi since the unit
of frequency in the SI is Hz. Thus, line 52 of 'maths_fns/jw_mapping.py'
must be removed.
2.
The frequency used for calculating the CSA seems not to be the
heteronuclear frequency. In fact, there is an error in lines 57 to 60
from 'maths_fns/jw_mapping.py' since the same item in the list is
assigned different values one after the other. Changing those lines
from :
self.data.frq_list[0, 1] = frqX
self.data.frq_list[0, 1] = frq - frqX
self.data.frq_list[0, 1] = frq
self.data.frq_list[0, 1] = frq + frqX
to :
self.data.frq_list[0, 1] = frqX
self.data.frq_list[0, 2] = frq - frqX
self.data.frq_list[0, 3] = frq
self.data.frq_list[0, 4] = frq + frqX
should work. The important thing is that item 1 stays the heteronuclear
frequency so it matches with line 1020 of 'maths_fns/ri_comps.py' :
data.csa_const_fixed[j] = data.frq_sqrd_list[j, 1] / 3.0
where the constant 'c' is calculated using the squared heteronuclear
frequency.
With those two modifications, I now get the same values as when
calculating manually or using Leo Spyracopoulos's Mathematica notebooks
(http://www.bionmr.ualberta.ca/~lspy/index_7.html).
Bye !
Sébastien :)
Edward d'Auvergne wrote:
Hi,
For the reduced spectral density mapping in relax, I have used
equations 10 to 12 from:
Markus M. A., Dayie K. T., Matsudaira P., and Wagner G. Local
mobility within villin 14T probed via heteronuclear relaxation
measurements and a reduced spectral density mapping. Biochemistry.
1996, 35(6):1722-32.
The equations themselves are derived from:
Lefevre J. F., Dayie K. T., Peng J. W., and Wagner G. Internal
mobility in the partially folded DNA binding and dimerization domains
of GAL4: NMR analysis of the N-H spectral density functions.
Biochemistry. 1996, 35(8):2674-86.
One problem may be that I made the assumption that the dipolar
constant of equation 7 of the first reference was missing the factor
of (mu0 / (4pi))^2! I based this assumption on the SI units
formulation of the R1, R2, and NOE equations and how the CSA constant
is defined. I think this is a fairly safe assumption though if you
look at equations 1, 2, and 8 of that paper.
Could the problem be the definition of the equations used? I've
looked at the code in relax and it seems to replicate these equations
correctly. Are the equations of Markus et al., (1996) correct? Is my
assumption about the dipolar constant correct? If you manually
calculate the reduced spectral density values using these alternative
equations, does relax produce the same values? I'm sorry that I can't
exactly pinpoint the problem, but something is seriously amiss.
Regards,
Edward
On 6/1/07, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/bugs/?9259>
Summary: Reduced spectral density mapping
yielding bad
values
Project: relax
Submitted by: None
Submitted on: Friday 06/01/2007 at 17:15 CEST
Category: relax's source code
Severity: 4 - Important
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name: Sébastien Morin
Originator Email: sebastien.morin.1@xxxxxxxxx
Open/Closed: Open
Discussion Lock: Any
Release: Repository: 1.2 line
Operating System: GNU/Linux
_______________________________________________________
Details:
Hi
I performed spectral density mapping on data recorded at three
magnetic
fields (500, 600, 800).
The values I get are erroneous (when compared with Leo Spyracopoulos'
Mathematica notebook which were manually verified using equations
from the
method 1 of Farrow et al., 1995, JBNMR, 6 : 153) and scaled depending
on the
magnetic field as shown in the table below (for which values
calculated using
either Leo's notebook or relax are divided by the value calculated
manually).
Field Method J(0) J(wN) J(wH)
===== ======= ========== ========== ==========
500 Farrow 1 (ref) 1 (ref) 1 (ref)
Leo 1 1 1
relax 0.04758 0.04757 0.999
600 Farrow 1 (ref) 1 (ref) 1 (ref)
Leo 1 1 1
relax 0.03361 0.03361 0.999
800 Farrow 1 (ref) 1 (ref) 1
Leo 1 1 1
relax 0.01932 0.01932 0.999
Then, if you take the different values for J(0) and J(wN) and compare
from
field to field, you get this :
J(0) J(wN) J(wH)
======== ======== ========
500/600 -> 1.415 1.415 1
500/800 -> 2.462 2.462 1
Those ratios are similar to what you get when comparing fields
quadratically
:
(600/500)^2 = (1.2)^2 = 1.44 ~ 1.415
(800/500)^2 = (1.6)^2 = 2.56 ~ 2.462
So there seems to be a problem somewhere in the calculations of
J(0) and
J(wN) and, to a lesser extent, J(wH)...
I first thought the problem was related with bug #9238... In fact,
before
this bug was solved, the problem was worst by a factor of ~2...
Still, the
skewing of Jw mapping results is quite important. Maybe is this
something
with the units or constants values...
Thanks for helping me !
Sébastien :)
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?9259>
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______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
Re: [bug #9259] Reduced spectral density mapping yielding bad values