[phenixbb] scattering factors
Goragot Wisedchaisri
goragot at u.washington.edu
Mon Jun 20 20:08:10 PDT 2011
Hi Ralf,
Hmm... You raised a very good point. Multiplying a_i by a constant would be the same effect as scaling Fcalc, and that should be fine as scaling is normally done during the refinement anyway. I will be curious to test this with electron diffraction data.
Hint: electron diffraction data to 1.9A resolution is available from pdb under accession code 2B6O.
George
On Mon, 20 Jun 2011, Ralf Grosse-Kunstleve wrote:
> 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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