[phenixbb] How does phenix.fmodel treat isotropic and anisotropic B?
zhangh1 at umbc.edu
zhangh1 at umbc.edu
Tue Sep 14 18:30:40 PDT 2010
Thanks a lot Pavel! I just double checked with your fomula for several PDB
with anisotropic B factors, and it is absolutely right, and my assumption
was just wrong.
Then, I think phenix.fmodel should consider only Uani in ANISOU line
(since Biso in ATOM line can be just derived, or redudant). However, as I
mentioned before, I set all Biso in ATOM lines to be 0 while keeping
ANISOU line unchanged. Now I think the results should be identical, but
numerically the output Fc is still different, although the maps are almost
the same. Not sure whether there is something more than that.
Finally, if Biso is just derived from Uiso, how is the residual B (say
after TLS refinement) considered?
Thanks again Pavel!
Best Regards, Hailiang
> 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, 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
>>
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