Hi,
Here are the different values I obtain for a residue with R1 = 1.1336 +-
0.0851 ; R2 = 12.9336 +- 0.9649 ; and NOE = 0.463921 +- 0.045
J(0) J(wN) J(wH)
===================== ===================== =====================
Here are the results with Leo Spyracopoulos's Mathematica notebook.
4.704231413115747e-9 2.664085520910741e-10 9.485555428699657e-12
Here are the results with relax without multiplying frequencies in Hz by
2 pi.
4.6978912534878238e-09 2.6603551824374712e-10
9.478993207668287e-12
ratio
0.9986522432526923179 0.9985997677461966745
0.9993081880043085706
Here are the results with relax when multiplying frequencies in Hz by 2 pi.
3.4634030539343071e-09 1.9612804482358541e-10
9.478993207668287e-12
ratio
0.7362314371436068543 0.7361927508863804185
0.9993081880043085706
The very small discrepancy we get (ratio 0.999...) is due to several
small differences in the definitions of constants (e.g. gn = -2.7126 in
relax and -2.7108 in Leo's notebook). This is not important. However,
there is a non negligible difference with the use of either frequencies
in Hz or frequencies transformed to rad/s.
Now, what do we do with that ?
The spectral densities are in units of rad / s = rad s^-1. (these are
not SI units, however)
The rates (R1, R2 and sigmaNOE) are in units of s^-1.
The constant 'd' is in units of s^-2.
The constant 'c' is in units of s^-2 also (or rad^2 s^-2 if we use
frequencies in rad s^-1, which are not SI units).
I now hesitate between 3 views.
1. Should the spectral densities be in SI units (i.e. in s, as the
frequencies are in s^-1 and the rates in s^-1) ?
2. If the spectral densities are in s rad^-1, the frequencies used to
calculate them should also be in rad s^-1, thus the constant 'c' should
be in rad^2 s^-2 and the constant 'd' also (so we should calculate it
without multiplying by the factor of (mu/4pi)^2). This would be about
using old units instead of the SI units, but then the spectral densities
would be in s rad^-1.
3. We could calculate everything in SI units (as we do right now) and
normalize to rs ad^-1 in the end.
Either way, I think that Leo's notebook yields spectral densities s and
not the usual s rad^-1 (as in the 2006 paper : JBNMR,36:215-224, for
which I calculated back spectral density values and yielded the same as
published where they say it's in s rad^-1, but the units deriving says
it's s).
Can you please tell me if I'm right with those ideas before I write to
Leo to report this apparent bug or typo or whatever...
Séb :)
Edward d'Auvergne wrote:
> Hi,
>
> That is awesome work tracking down this problem. Thank you! I'll
> apply your patch and then hopefully make a new relax 1.2 release with
> your fixes very soon. I do have a important question first though.
>
> My question relates to the multiplication of the frequency by 2pi to
> convert from Hz to rad/s units. The symbol for the frequency in Hz is
> nu whereas the frequency in rad/s is omega. In all the relaxation
> equations composed of spectral density components, the frequencies are
> in rad/s and are represented by the omega symbol. This includes the
> CSA constant defined in SI units as
>
> c = (omegaX.CSA)^2/3,
>
> where CSA is the chemical shift anisotropy and
>
> omegaX = gammaX.B0.
>
> To get nuX which is the frequency of the X nucleus in Hz, omegaX
> measured in rad/s should be divided by 2pi. So my question is, do you
> get the same results as the Mathematica notebooks of Leo Spyracopoulos
> if you retain the multiplication of the frequency by 2pi?
>
> Thanks,
>
> Edward
>
>
> P.S. The problem with the list of frequencies is probably the major
> issue. I'm not sure why I attempted to fill out the entire list of
> frequencies as the reduced spectral density mapping code only uses the
> value in self.data.frq_list[0, 1], the frequency of the heteronucleus,
> to calculate the CSA constant. The higher frequencies are never used
> in the calculation. Anyway, your patch fixes this problem.
>
>
>
>
> On 6/13/07, Sebastien Morin <[EMAIL PROTECTED]> wrote:
>> 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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED]
>> >> 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>
>> >>
>> >> _______________________________________________
>> >> Message sent via/by Gna!
>> >> http://gna.org/
>> >>
>> >>
>> >> _______________________________________________
>> >> relax (http://nmr-relax.com)
>> >>
>> >> This is the relax-devel mailing list
>> >> relax-devel@gna.org
>> >>
>> >> 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-devel
>> >>
>> >
>> >
>>
>> --
>> ______________________________________
>> _______________________________________________
>> | |
>> || 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 |||
>> || ||
>> |_______________________________________________|
>> ______________________________________
>>
>>
>>
>
--
______________________________________
_______________________________________________
| |
|| 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 |||
|| ||
|_______________________________________________|
______________________________________
_______________________________________________
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