Filip Van Petegem wrote:
In a case I'm currently looking at, I'm particularly dealing with cryo-EM data,
not X-ray structures, but with the same underlying principles: what are the
odds that all pixels of the map move together in the same direction?
I suspect you may be better off asking an EM person (or on an EM list),
due to the peculiarities of cryo-EM reconstruction. If I'm recalling
correctly, EM resolution is determined by Fourier shell correlation so
it might not have a one-to-one relationship to optical resolution. In
addition, there usually is some uncertainty in converting voxel
distances to physical distances - so an optical resolution in terms of
Anstroms would need to be converted.
As a few others have pointed out, you'd also need to account for
coordinate uncertainty. For 3d reconstruction, you've got uncertainties
from particle image classification, image alignment, possibly
conformational heterogeneity, and possibly uncertainties in the voxel
position (due to interpolation) and voxel values (and the voxel to
Angstrom conversion). My understanding of EM is limited to what I need
to know to deal with EM data from collaborators, or how to use some EM
software with low-resolution x-ray data - so I may be missing a few
things (or pointing out problems that have been dealt with).
The short version, or at least my take on it, is that you may not be
able to get a mathematically/statistically rigorous test for if the
movement of a set of voxels is significant or not - but asking an EM
person could probably give you a better answer.
Pete
As mentioned for X-ray structures, a Luzzati analysis may give information
about the positional errors, but there should be an increased resolution when
comparing domain movements, because it's unlikely for all atoms to have an
error in the same direction.
Filip
On Mon, Nov 21, 2011 at 2:16 PM, Jacob Keller
<[email protected]<mailto:[email protected]>> wrote:
Just to clarify: I think the question is about the mathematical sense
of "significance," and not the functional or physiological
significance, right? If I understand the question correctly, wouldn't
the reasoning be that admittedly each atom in the model has a certain
positional error, but all together, it would be very unlikely for all
atoms to be skewed in the same direction?
Jacob
On Mon, Nov 21, 2011 at 4:04 PM, Filip Van Petegem
<[email protected]<mailto:[email protected]>> wrote:
Dear crystallographers,
I have a general question concerning the comparison of different
structures. Suppose you have a crystal structure containing a few domains.
You also have another structure of the same, but in a different condition
(with a bound ligand, a mutation, or simply a different crystallization
condition,...). After careful superpositions, you notice that one of the
domains has shifted over a particular distance compared to the other
domains, say 1-1.5 Angstrom. This is a shift of the entire domain. Now
how can you know that this is a 'significant' change? Say the overall
resolution of the structures is lower than the observed distance (2.5A for
example).
Now saying that a 1.5 Angstrom movement of an entire domain is not relevant
at this resolution would seem wrong: we're not talking about some electron
density protruding a bit more in one structure versus another, but all of
the density has moved in a concerted fashion. So this would seem 'real',
and not due to noise. I'm not talking about the fact that this movement
was artificially caused by crystal packing or something similar. Just for
whatever the reason (whether packing, pH, ligand binding, ...), you simply
observe the movement.
So the question is: how you can state that a particular movement was
'significantly large' compared to the resolution limit? In particular, what
is the theoretical framework that allows you to state that some movement is
signifcant? This type of question of course also applies to other methods
such as cryo-EM. Is a 7A movement of an entire domain 'significant' in a
10A map? If it is, how do we quantify the significance?
If anybody has a great reference or just an individual opinion, I'd like to
hear about it.
Regards,
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267<tel:%2B1%20604%20827%204267>
email: [email protected]<mailto:[email protected]>
http://crg.ubc.ca/VanPetegem/
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [email protected]<mailto:[email protected]>
*******************************************
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: [email protected]<mailto:[email protected]>
http://crg.ubc.ca/VanPetegem/
