On 10/01/12 13:25, Luca Pellegrini wrote:
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 believe that the maps are not available via the web server interface.
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.
Some people still do...
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?
The maps *are* calculated (AFAIK).
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
What would you rather it say, I'm happy to change the message. "The EDS
does not think that this is a reliable map, in that it is or may be
inconsistent with what the authors were looking at during deposition"?
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.
Mark Harris got in touch with me. He himself had been contacted by an
(irate?) depositor of a lactose permease who was aggrieved that the map
one could download from the EDS via Coot had no indication about it that
the map was different to the one he was looking at. That, at least, was
what I understood the complaint to be about.
So Coot now accesses the EDS page for each accession code now and screen
scrapes it to determine if the EDS gives a convention statistics page -
or a warning about unreliability. I'm sorry that that was not good enough.
Paul.
