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I am very glad that Geoffrey Chang and his group were able to discover
their mistake and to let everyone know about it. I would like to expand
slightly upon the many excellent points that have already been made:
1. It is essential that the crystallographic community agree to require
deposition of all the data necessary to re-analyze an experimental
result. This means (at a minimum) that anomalous data for a SAD
experiment, or the actual model used for a molecular replacement solution
must be deposited. If this had been done in this case, others could have
discovered the problem and possibly even corrected it. The deposition of
images might be more difficult, and I do not think that these are as
essential as processed data in most cases, but in this case deposition of
images could have helped as well.
2. The display of omit maps in which a model has never been used in the
omitted region should be a standard procedure in our field. An omit map of
this kind does not provide the most accurate picture of a region of a map,
but it provides the only known method for producing a picture that is
certain to have no model bias. It is not difficult to create such a map:
if you carry out molecular replacement, you can do a parallel run in which
your search model has a section removed -- and look at all your maps in the
region where there was no search model. These maps should be required by
journals and expected by reviewers. In cases where this is too
time-consuming, composite SA-omit maps and related procedures also greatly
reduce model bias. Some procedure of this type should be used to check any
structure in which the experimental phasing does not provide an unambiguous
picture of the structure (e.g., in many low-resolution experimental maps
and in all MR maps).
All the best,
Tom Terwilliger
At 01:32 PM 12/23/2006 -0500, Arun Malhotra wrote:
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I was shocked to see the retraction in yesterday's issue of Science (Dec
22, 2006) of several ABC transporter structures and papers from the Chang
lab, including three published in Science. The retraction says that the
structures have the wrong hand and topology due to an "in-house" program
that inverted the signs on the anomalous pairs.
I have no expertise in ABC transporters, but were there warning signs in
the structures? Were red flags raised by PDB or the other servers such as
EDI, EDS, etc.? Looking at some of these papers, these are low resolution
structure and I see very high R/Rfree, but there must have been other
signs of problems as well.
In the past few years, there have been almost no structures retracted due
to gross errors and the checks being used by structural biology community
seemed to working quite well - what can we learn from this tragic and sad
error ?
--
Arun Malhotra Phone: (305) 243-2826
Associate Professor Lab: (305) 243-2890
Dept. of Biochemistry & Molecular Biology Fax: (305) 243-3955
University of Miami School of Medicine
PO Box 016129 E-Mail: [EMAIL PROTECTED]
Miami, FL 33101 Web: http://structure.med.miami.edu
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: [EMAIL PROTECTED]
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site:
http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
