In fact, if you want the truth, what I now do is to download the sf.cif file,
use ccp4i to regenerate the MTZ (with the same Free R-factor flags that the
authors have used for structure refinement). Then feed that into Phenix for a
few rounds of positional and temperature factor refinement with
Dear Fred,
People have already done this for all PDB entries:
- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats
- http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the
stats and maps do improve most of the time, unfortunately also for
structures that are not
Yes, totally agree that the good thing about it all is that the problems
have been identified and the wrong data will hopefully be eliminated. Shame
it took almost 10 years since the first fabricated structure was published
and more then 2 since questions were first risen about this work...
Paula
Dear Fred,
People have already done this for all PDB entries:
- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats
- http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the
stats and maps do improve most of the time, unfortunately also for
structures that are not
I agree with Randy Read though - it's a mistake to get too carried away
with the foul-play aspect of this. There were clearly very serious
problems with those structures anyway. What it shows is that you can
desposit just about anything in the PDB, which is quite worrying when you
consider how
On Sat, 12 Dec 2009 11:58:27 +0530 Dr. Anthony Addlagatta wrote:
Bernhard,
I would be worried about sending the structure factors and the coordinates
along with
the manuscript.
I wonder why?
Cheers
Fred
From a statistical point of view, there could be a rare bad apple reviewer
as well as a rare bad apple (fraud intending) author. Life is inherently
risky
but we still cross streets.
More important, science is based on accessibility of primary data
and reproducibility of results. Without primary
A number of years ago - we were asked to setup an ftp site a particular
reviewer could see the coordinates... I could have looked at the logs to
figure out where they were coming in from but chose not to. Some
journals also allow the author to upload additional info - that would be
available
Dear Eric Bennett,
3g6a was processed by PDB_REDO (without the original R-free set which
sadly wasn't deposited) on Monday, 20 July 2009 at 21:35 CEST with
PDB_REDO version 2.6: http://www.cmbi.ru.nl/pdb_redo/g6/3g6a/index.html
That was roughly two months after the last revision (the entry is
Robbie Joosten wrote:
I think the deposition of maps is a waste of space. Maps may describe what
the depositors paranoidwant you to think they/paranoid have looked at.
But that does not mean they looked at the right thing. Who knows what they
did to the maps in terms of (unwarrented) density
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