On 8 Apr 2012, at 21:18, aaleshin wrote:
What I suggested with respect to the PDB data validation was adding some
additional information that would allow to independently validate such
parameters as the resolution and data quality (catching of model fabrications
would be a byproduct of
Thank you Phil, for clarification of my point, but it appears as cheating in a
current situation, when an author has to fit a three dimensional statistics
into a one-dimentional table. Moreover, many of journal reviewers may never
worked with the low-resolution data and understand importance of
How about such a footnote to Table 1:
The resolution of data is 3A in the a direction, 3.5A in b direction and 5A
in the c direction
Wouldn't this do the trick?
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
I've done that in papers
The more fundamental problem is in the end what we want to know are things like
is residue 43 close to residue 146?, which side chains interact with the
ligand? etc etc and resolution is only a very rough guide to the correctness
of such conclusions
Phil
On 9 Apr
On 04/09/12 12:32, Boaz Shaanan wrote:
How about such a footnote to Table 1:
The resolution of data is 3A in the a direction, 3.5A in b direction and 5A in
the c direction
Wouldn't this do the trick?
Usually there's a requirement for a table of statistics, including
completeness and R in
It is a wonderful server indeed, but its default setting cuts the resolution at
3 sigma (if I remember correctly). It is too stringent in my opinion. Also, it
is not clear to me whether to submit all data to the highest resolution point,
or the data that come from the server? But then again,
On Apr 9, 2012, at 11:47 AM, aaleshin wrote:
Thank you Phil, for clarification of my point, but it appears as cheating in
a current situation, when an author has to fit a three dimensional statistics
into a one-dimentional table. Moreover, many of journal reviewers may never
worked with
Hi Alex,
It is not clear to me how to report the resolution of data when it is 3A
in one direction, 3.5A in another and 5A in the third.
can't be easier I guess: just switch from characterizing data sets with one
single number (which is suboptimal, at least, as Phil pointed out earlier)
and
Hi Pavel,
Reporting the table that you suggested would create more red flags for the
reviewers and readers than explaining how to understand the resolution of my
data. We need more studies into this issue (correlation between the resolution
of anisotropic data and model quality). And there
Alex,
I think you are mixing two things here: presenting statistics that
characterizes the data and its interpretation.
Looking at data completeness as a single number tells something but not a
lot, while looking at these metrics per resolution reveals a whole lot more
information (for example,
Or as tensor, see classic:
ANISOTROPIC SCALING OF 3-DIMENSIONAL INTENSITY DATA
Author(s): SHAKKED, Z (SHAKKED, Z)
Source: ACTA CRYSTALLOGRAPHICA SECTION A Volume: 39 Issue: MAY Pages:
278-279 DOI: 10.1107/S0108767383000665 Published: 1983
I guess this or similar is implemented in
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