[phenixbb] scattering factors
Ralf Grosse-Kunstleve
rwgrosse-kunstleve at lbl.gov
Mon Jun 20 17:56:51 PDT 2011
Hi George,
> No, the factor m/m0 is independent of atom types
Can anomalous (f') and dispersive (f") contributions be ignored?
Ignoring these the structure factor equation is
f_calc += f0 * dw * occ * sym_weight * exp(2 * pi * i * x * h)
dw = isotropic or anisotropic Debye-Waller factor
occ = occupancy factor (between 0 and 1)
sym_weight = usually 1 except for special positions
x = fractional coordinate of atom
h = Miller index
f0 = Sum[a_i * exp(-b_i * stol**2)]
If you scale all the a_i by a constant factor, it is the same as
scaling the final f_calc by the same constant factor. Therefore the
m/m0 will just change the overall isotropic scale factor, which we
determine dynamically inside phenix.refine; the value isn't usually
interesting. I.e. I'd expect that you can use phenix.refine as-is.
But maybe I'm missing something important? I've never worked with
electron diffraction data.
Ralf
On Mon, Jun 20, 2011 at 1:45 PM, Goragot Wisedchaisri
<goragot at u.washington.edu> wrote:
> Hi Ralf,
>
> No, the factor m/m0 is independent of atom types for the same acceleration
> voltage (m0 is electron rest mass, m is relativistic mass of electron which
> depends on acceleration voltage. The Guassian ai and bi coefficients already
> take care of fitting scattering factor f(e) for each atom type. In another
> word, if you can implement a function that calculates and multiplies m/m0 to
> all the ai coefficients for all atom types in the table, users will only
> need to input the acceleration voltage.
>
> Thanks,
>
> George Wisedchaisri
>
>
> On Mon, 20 Jun 2011, Ralf Grosse-Kunstleve wrote:
>
>> Hi George,
>>
>>> I have a question though. Because electron scattering depends on the
>>> velocity of the electron which in turn depends on the acceleration
>>> voltage
>>> of the microscope. The gaussian parameters need to be corrected using the
>>> relativistic electron velocity by multiplying the ai parameters with m/m0
>>> =
>>> (1 – v2/c2) ^-1/2 where v is the relativistic electron velocity and c is
>>> the
>>> velocity of light (for example m/m0 = 1.58707 for a 300keV electron
>>> microscope).
>>
>> Is the factor m/m0 different for each atom type?
>>
>> Ralf
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>
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