Dear Asmita, (and all who may be interested)
In Gourinath & Himmel et al. Structure 11:1621-1627 (2003), I normalized
B-factors
of several crystal structures for comparisons, using a simple applications of
statistics.
Any such analysis must be viewed with caution, of course, because it relies
Hi,
also keep in mind that the total model structure factor used in refinement
and anywhere where model-to-data agreement needs to be evaluated (such as
maps or R factors) is:
Fmodel = ktotal * (Fcalc_atoms + F_bulk_solvent + F_something_else)
where ktotal ~ scale * exp(-h*Uoverall*h_transpose)
Woops, sorry. There was a typo in my response. here it is again
without the typo.
B factors are 78.96x the value of the mean square variation in an atom's
position. The square is the important part of how you scale them. Lets
say you have static disorder in the crystal lattice, and that gi
B factors are 78.96x the value of the mean square variation in an atom's
position. The square is the important part of how you scale them. Lets
say you have static disorder in the crystal lattice, and that gives
every atom an rms variation of 0.5 A relative to their ideal lattice
positions, t
Hi Asmita,
Try running your different crystal structures through PDB_REDO. That should
normalize the B-factors to some meaningful values for comparison.
Best wishes,
Avinash
On Wednesday, 02 August, 2017 21:58:07 Asmita Gupta wrote:
> Hi,
>
> Thanks for the response!
>
> What I have are crystal structures of the same protein in multiple
> conformations, solved by different groups. I wanted to calculate the
> residue-wise B-factors for each of these structures and
Hi,
Thanks for the response!
What I have are crystal structures of the same protein in multiple
conformations, solved by different groups. I wanted to calculate the
residue-wise B-factors for each of these structures and compare how the values
are changing for corresponding residues in these
On Wednesday, 02 August, 2017 12:09:35 Asmita wrote:
> Hi,
>
> This might look as a very fundamental question. I have a dataset of crystal
> structures better than 3.5Ang resolution. For a qualitative analysis, I
> want to compare the residue-wise B-factors in these structures, but due to
> differ
Hi,
This might look as a very fundamental question. I have a dataset of crystal
structures better than 3.5Ang resolution. For a qualitative analysis, I
want to compare the residue-wise B-factors in these structures, but due to
different procedures adopted in refinement and scaling, I understand th
