There can be many different reasons why EDS calculates an R-value that is
different from the one reported by the authors - some of these are listed
here: http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS
Back in the "dark ages" (actually, the late 90s) we arbitrarily decided to use
a tolerance of 5 percentage points. If the difference is greater, we assume
that -as some people have subtly put it- we are a bunch of incompetent morons
who can't even calculate a map, and we choose not to make the maps and
statistics derived in the process of calculating them available. So, if
anything, the phrase "unreliable map" means just that - we cannot be sure that
we have done a good job at calculating the map, and would rather be safe than
sorry.
Once upon a time, we asked crystallographers to help us trace the causes of
any discrepancies for their entries so that we could improve EDS and the
public archive. However, no good deed goes unpunished (ask Colin), and this
request resulted in so much abuse from several prominent crystallographers
(incl. a Nobelist) that we abandoned that effort. (I don't think any of them
had actually tried to download the coordinates and structure factors from the
PDB and calculate maps from those themselves... one of them subsequently tried
and found himself unable to reproduce his own R-value...)
Nowadays, EDS in Uppsala is unfunded and unstaffed. It is an automatic script
that runs every weekend. Obviously, that means that we cannot offer support,
let alone do new development work. In the future, EDS will rise from its ashes
at PDBe - at that stage, we can reconsider many choices we made for the
Uppsala version and will also have resources to maintain and support it
properly.
--Gerard
Dear all,
A minor point but worth mentioning, I think...
The EDS server does not produce a density map for PDB entries for which it
cannot calculate R-factors within 5 percentage points of the published
values. I understand that the server was set up in the dark ages of
crystallographic refinement, when people perhaps took some liberties with
their refinement protocols. Hopefully, the educational point now has been
made so wouldn't it be better to calculate the map together with a warning
of the discrepancy in R-factor values?
Coot does display a map for such a PDB entry, but with a pop-up window
warning the user that "This is not a reliable map." Without explanation,
this statement is at least as unreliable as the map that it refers to and
bound to confuse and alarm the user who - in the large majority of cases -
finds himself/herself staring at a perfectly decent (reliable?) map.
Luca
Luca Pellegrini
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA - UK
Email: lp...@cam.ac.uk
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59
Best wishes,
--Gerard
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Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
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