Hi Rajesh,
model bias, in a nutshell, is when you see something in the map that
is conveyed by the model (that may not be correct) and not by the
data.
I am not sure how one can get an idea about model bias looking at
triplet of numbers: Rwork, Rfree and Molprobity percentile. By the
way, your Rwork/Rfree look pretty good (given the 2.7A resolution).
Anyway, if everything else: bunch of model and data statistics,
local and global model-to-data quality fit all look well (*), and
you are still suspecting something isn't right, then you can invest
from a few days to a week or so into computing an "Iterative Build
OMIT map" as described here:
Iterative-build OMIT maps: map improvement by iterative model
building and refinement without model bias. T. C. Terwilliger, R. W.
Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J.
Read, P. H. Zwart and L.-W. Hung Acta Cryst. D64, 515-524 (2008)
This map is supposed to be bias free.
Pavel
(*) For more details see here:
http://www.phenix-online.org/presentations/latest/pavel_validation.pdf
I have a
structure 2.74 A structure with R/freeR 22.7/27.9%. But the
molprobity score is 50th percentile.
If I
fix the outliers they wouldn't go away and molprobity score
remains same or get worst.
This
structure was solved by molecular replacement using a
bacterial protein with 38% identity.
I am
wondering if there is an model bias? I have not identified
particular region in model for bias.
My
questions are: Am I right in thinking if there is model bias
based on above info?
I
added my .pdb and .mtz and do SA-composit omit map. This is
running from morning and I have feeling that I will get
results after thanksgiving. Is this the correct way of doing
a omit map for the purpose I mentioned?
I saw
lot of discussions on omit map but couldn't grasp everything
and I am sure same questions might have been asked before.
I
have couple of classical papers next to me but I need help.
I would appreciate if you could
help me out either suggesting me how and what to do or
pointing to previous thread over the this BB.