[phenixbb] Question regarding phenix.fmodel
zhangh1 at umbc.edu
zhangh1 at umbc.edu
Mon Apr 25 14:55:39 PDT 2011
Hi Pavel:
Actually they differs about 3% at the same reflection point by using MTZ
or not. If I use direct summation (for 15 atoms), they differ even more
(~10%). At this point I assume the without MTZ one is more pure fmodel
calculation, but just let me know for any comments.
For the h0k0l0 issue, I just figured out that phenix.fmodel does take this
point, and it was phenix.cif_as_mtz which deleted this point. Sorry about
the confusion.
Hailiang
> Hi Hailiang,
>
>> According to the instruction, phenix.fmodel was supposed to calculate Fc
>> only;
>
> not just Fc, but Fmodel; phenix.fmodel is to compute model structure
> factors:
>
> Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4)
> * Fmask)
>
> where:
>
> - Fmodel - total model structure factor (complex value)
> - AnisoScale = -ht*A(-1)*b_cart*A(-1)th/4
> - h - column vector with Miller indices
> - A - orthogonalization matrix
> - b_cart - anisotropic scale matrix
> - t and (-1) denotes transposition and inversion operations
> - scale - overall scale factor
> - Fcalc - structure factors calculated from atomic model
> - k_sol and b_sol - Flat Bulk solvent model parameters
> - Fmask - structure factors calculated from bulk solvent mask
>
> When you run like this
>
> phenix.fmodel model.pdb high_res=XX
> or
> phenix.fmodel model.pdb some_data.mtz
>
> then k_sol=b_sol=AnisoScale = 0, and obviously Fmodel = Fcalc
>
>> however, when I try the following 2 scripts, they ended up with
>> different Fc values (at the same hkl point):
>>
>> 1. phenix.fmodel ${PDB} high_resolution=XX
>> 2. phenix.fmodel ${PDB} ${MTZ}
>>
>> The instruction says (2) will output Fcalc that will match the set of
>> Miller indices of the data in reflection_data.mtz file, so I thought 1
>> and
>> 2 should have the same values at the same hkl points...
>
> How different they are? If very slightly then this is expected. They
> must be identical if you use this keyword: "algorithm=direct" (the
> default is "algorithm=fft"). However, using the direct summation
> algorithm for structure factors calculation may take a long time
> (depending on data/model size). As a quick test you can leave in your
> PDB file a few atoms, then run with "algorithm=direct" and see if both
> ways give you the exact same Fmodel values. Let me know otherwise and I
> will have a closer look (I would probably need the inputs in this case).
>
>> (A most direct way would be checking the Fc at h0k0l0 point and see
>> whether they are proportional to the molecular size, but it seems
>> phenix.fmodel will ignore this point even I expicitly add it to the MTZ
>> file.)
>
> Hm.. I'll check this.
>
> Pavel.
>
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