Hi Filip,
Would it be a worth-while exercise to make a histogram of the absolute
values of atomic displacements ? If the distribution is bimodal (as you
indicated that it may), then indicating statistical significance should be
much easier (and convincing ?).
My twocents,
Nicholas
On Mon,
** Sorry for posting again, but I wanted to replace the subject by the
specific topic (my former subject was due to the dact that I use the
CCP4BB digest only) **
Dear Filip,
as Roberto mentioned earlier, our program Escet, respectively the RAPIDO
web server -
Dear Filip
'Annoying' MR problems for which the answer often lies in relatively small
differences between the search model and 'RB-shifted' domains and/or subdomains
in the actual structure, are I think a good experimental indication of the
significance of such issues.
To extrapolate from
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
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
I believe ESCET was designed to answer your kind of question
Best
Roberto
On 21 Nov 2011, at 22:03, Filip Van Petegem
filip.vanpete...@gmail.commailto:filip.vanpete...@gmail.com wrote:
Dear crystallographers,
I have a general question concerning the comparison of different structures.
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
Hello Jacob,
that's correct, I'm only looking at the mathematical significance, not the
biological one. I follow the same reasoning - it is highly improbably for
all atoms to be skewed in the same direction.
In a case I'm currently looking at, I'm particularly dealing with cryo-EM
data, not
On Nov 21, 2011, at 3:04 PM, Filip Van Petegem wrote:
So the question is: how you can state that a particular movement was
'significantly large' compared to the resolution limit?
I can think of a different but related question. How significant is a
particular movement compared to a measured
This is a subtle problem and performing an analysis of this type
of error is confusing. Most of the tools we use to analyze errors
begin with the assumption that the errors are random and uncorrelated.
These include Luzzati and Fo-Fc maps.
My solution is to perform a null hypothesis test.
On Nov 21, 2011, at 3:52 PM, Filip Van Petegem wrote:
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
On Nov 21, 2011, at 5:23 PM, James Stroud wrote:
except that you use Euclid's formula to calculate the distances in higher
dimensions
I meant to say Euclidian distance. Euclid's formula has a specific meaning
that is different.
I am curious how all of this can be more than splitting hairs, i.e.,
under what conditions can this 1Ang domain motion mean something
biologically significant? Proteins are pretty flexible, after all,
especially between domains.
JPK
On Mon, Nov 21, 2011 at 6:41 PM, James Stroud
On Nov 21, 2011, at 6:34 PM, Jacob Keller wrote:
I am curious how all of this can be more than splitting hairs, i.e.,
under what conditions can this 1Ang domain motion mean something
biologically significant?
To engage in the discussion, I think we had to accept this:
On Nov 21, 2011, at
If the difference in likelihood is quite small then you cannot distinguish
between a RB shifted model and one w/o the shift and that shift must be
insignificant (in a statistical sense.) If the likelihood is better when
the shift is allowed then the shift is significant.
That of course is
A mixture between mathematical significance and biological significance
as a part of the reply:
you should also take into account the thermal vibrations of the atoms
present in that domain, i.e. the thermal ellipsoids when you have one
of the representations of anisotropic temperature factors
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