How does phenix.fmodel treat isotropic and anisotropic B?
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
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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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, [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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Hi Hailiang,
Then, I think phenix.fmodel should consider only Uani in ANISOU line (since Biso in ATOM line can be just derived, or redudant).
correct, and this is exactly what I wrote in my previous reply. Here is copy-paste: """ 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. """
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,
The results must be identical, it not, then I can't explain it without having more information.
Finally, if Biso is just derived from Uiso, how is the residual B (say after TLS refinement) considered?
The answers are here: http://journals.iucr.org/j/issues/2002/04/00/ks0128/index.html http://www.phenix-online.org/newsletter/ Pavel.
Hi Pavel: I just found that the PDB structure I tested has very small part isotropic B, and my program set them to 0 as well. Now I am clear that phenix.fmodel check each atom for anisotropic B: if has, ignore the isoB, if not, take the isoB. Sorry for the confusion due to my careless about the small part isotropic B (hard to find though:( Best Regards, Hailiang
Hi Hailiang,
Then, I think phenix.fmodel should consider only Uani in ANISOU line (since Biso in ATOM line can be just derived, or redudant).
correct, and this is exactly what I wrote in my previous reply. Here is copy-paste:
"""
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.
"""
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,
The results must be identical, it not, then I can't explain it without having more information.
Finally, if Biso is just derived from Uiso, how is the residual B (say after TLS refinement) considered?
The answers are here: http://journals.iucr.org/j/issues/2002/04/00/ks0128/index.html http://www.phenix-online.org/newsletter/
Pavel.
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Hi Hailiang, ok, great! I'm glad you sorted this out. Pavel. On 9/15/10 10:22 AM, [email protected] wrote:
Hi Pavel:
I just found that the PDB structure I tested has very small part isotropic B, and my program set them to 0 as well. Now I am clear that phenix.fmodel check each atom for anisotropic B: if has, ignore the isoB, if not, take the isoB.
Sorry for the confusion due to my careless about the small part isotropic B (hard to find though:(
Best Regards, Hailiang
Hi Hailiang,
Then, I think phenix.fmodel should consider only Uani in ANISOU line (since Biso in ATOM line can be just derived, or redudant). correct, and this is exactly what I wrote in my previous reply. Here is copy-paste:
"""
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.
"""
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, The results must be identical, it not, then I can't explain it without having more information.
Finally, if Biso is just derived from Uiso, how is the residual B (say after TLS refinement) considered? The answers are here: http://journals.iucr.org/j/issues/2002/04/00/ks0128/index.html http://www.phenix-online.org/newsletter/
Pavel.
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Pavel Afonine -
zhangh1＠umbc.edu