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

Pavel Afonine pafonine at lbl.gov
Tue Aug 31 22:06:56 PDT 2010

```  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
- Fmask - structure factors calculated from bulk solvent mask

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:
>
>     use_asu_masks = False
> }
>
> 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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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

```