Thank you Randy and Pavel for correcting my failure to find an
appropriate tool in my mental toolbox. I was thinking too much
in terms of examining a difference map rather than a performing
a resolution-dependent analysis of Fo;Fc agreement.
Is there a straight-forward way to extract what Hunter
Randy,
Use of correlation makes normalization superfluous, but as you say it
cannot distinguish from the causes of deviation which may not just be
missing density.
Pavel,
Thanks for the reference. Will look at it more closely.
But how is the error being separated into separate error components
Hi,
Is there a straight-forward way to estimate the amount of missing electron
> density that a particular protein structure is missing based on the
> difference between Fo and Fc?
>
Any refinement or map calculation software that uses likelihood-based
approach does this routinely. In
Hi,
I rarely disagree with Ethan, but there are in fact ways of getting some idea
of how much of the ordered structure from your crystal is missing in your
model. It's not based on the difference between Fo and Fc but rather more on
the correlation between them and how that varies as a
This is a good point, the difference between Fo and Fc can be great if Fc is
actually missing (an 'incomplete' structure). And of course this wreaks havok
in defining the maskf for bulk solvent, and refinement, etc. Incomplete can be
missing whole parts of the protein (say in model building) or
Ethan and Phil,
Your responses about i) normalization based on minimizing the average
differences between Fobs and Fcalc and ii) the smearing of electron density
by various physical phenomena, makes sense.
The smearing cannot easily be accounted for and having density, where it
should not be, can
On Tuesday, 21 February, 2017 16:53:06 Hunter Moseley wrote:
> Is there a straight-forward way to estimate the amount of missing electron
> density that a particular protein structure is missing based on the
> difference between Fo and Fc?
Short answer: no.
> It appears that the normalization
Is there a straight-forward way to estimate the amount of missing electron
density that a particular protein structure is missing based on the
difference between Fo and Fc?
It appears that the normalization of the Fc due to the employing of a
maximum entropy method that keeps Fo and Fc comparable
