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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