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                          |||
>    ||                                               ||
>     |_______________________________________________|
>          ______________________________________
>
>
>

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