[phenixbb] How does phenix.fmodel treat isotropic and anisotropic B?

Pavel Afonine pafonine at lbl.gov
Tue Sep 14 17:01:58 PDT 2010

  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)


   - 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.


On 9/14/10 4:48 PM, zhangh1 at umbc.edu 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list