# [phenixbb] How to do a phenix.fmodel calculation incorporating the exponential scaling model only?

zhangh1 at umbc.edu zhangh1 at umbc.edu
Tue Aug 31 22:25:46 PDT 2010

```Thanks Pavel! The reason I want to try exp scaling is because I somehow
cut my model into different parts, and I am afraid flat model will
double-count partial protein-solvent interface when I add'em up. Thanks
anyway!

Best Regards, Hailiang

>   Hi Hailiang,
>
> it has been shown that Flat Bulk-Solvent Model is better than
> exponential model:
>
> Jiang, J.-S. & Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115.
> "Protein hydration observed by X-ray diffraction. Solvation properties
> of penicillopepsin and neuraminidase crystal structures."
>
> A. Fokine & A. Urzhumtsev. Acta Cryst. (2002). D58, 1387-1392. "Flat
> bulk-solvent model: obtaining optimal parameters"
>
> P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005).
> D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling
> procedure"
>
> so phenix.fmodel, phenix.refine, phenix.maps, phenix.model_vs_data and
> other similar tools all use mask based (Flat Model) for bulk solvent.
>
> The exponential model is not available.
>
> If you type phenix.fmodel and hit Enter the screen output tells you the
> total model structure factor formula:
>
>    Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4)
>
>    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
>
>
> Pavel.
>
>
>   On 8/31/10 9:55 PM, zhangh1 at umbc.edu wrote:
>> Hi,
>>
>> I want to use phenix.fmodel to do a calculation incorporating the
>> exponential scaling model only (Not the flat model). I am not sure
>> whether
>> I just need simply specify:
>>
>> }
>>
>> since the output maps are just identical no matter use_asu_masks = True
>> or
>> False. Should I do something else to enable exponential scaling model
>> only? Thanks!
>>
>> Best Regards, Hailiang
>>
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>
>
>

```