Hi Hailiang, all phenix.fmodel uses from input PDB file are: - CRYST1 record; - Coordinates, occupancies and scattering types from ATOM records; - ADPs defined in ANISOU records (if ANISOU records are available) or it takes isotropic equivalent from ATOM records. That's all you need to compute Fcalc (but not Fmodel), which is: 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 Note, the isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2. Pavel. On 9/14/10 4:48 PM, [email protected] wrote:
Hi,
I am doing a phenix.fmodel calculation for a PDB structure containing anisotroipc B. If I understand it correctly, the B factor is composed of both the isotropic B for ATOM line (Biso) and the anisotropic B from ANISOU line (Uani):
Fc=sigma ( fi * exp (-Biso*s*s) * exp (-st*Uani*s) * exp (i*r*s) )
Please correct me if the above equation is wrong. I also noticed that in PDB, the Uani (after scaling by 10^-4) is generally much smaller than Biso. So I assume that Biso has a much bigger contribution than Uani, the latter only implying the vibrational anisotropicity.
However, I did a test calculation by setting all Bio to 0 whereas keeping Uani unchanged. Due to the above assumption, I expected the results should be very different from the native structure; however, coot told me they were just so close...
Maybe I am wrong somewhere...
Best Regards, Hailiang
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