How to do a phenix.fmodel calculation incorporating the exponential scaling model only?
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: mask { 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
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) * 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 Pavel. On 8/31/10 9:55 PM, [email protected] 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:
mask { 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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) * 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
Pavel.
On 8/31/10 9:55 PM, [email protected] 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:
mask { 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Pavel Afonine -
zhangh1＠umbc.edu