[ccp4bb]: Re: structure factors/quality control

["Ulrich K. Genick" <genick@brandeis.edu>]

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The majority of the debate about the structure
factors boils down to the integrity of the PDB
data base and what we can do to keep it up
or even improve it.

The usefullness of the PDB for crystallographers
and non-crystallographers alike relies on the
reliability of the structures deposited in it.

Bad structures, along with structure factors,
which can be used to prove that those structures
are bad, are only marginally better than
bad structures alone. In particular non-
crystallographers do not have the expertise
or tools to use the structure factors any way.

Peer review, as frustrating as it can be, has
proven to be the only viable quality-control
tool in science.

And by peer review I do not
mean a mob of crystallography vigilantes perusing
the PDB to revel in their competitors (maybe honest)
mistakes.

Here are some things we can all do to
as our part in the peer reveiw quality control
system:

- In our role as reviewers:
   WE HAVE TO INSIST THAT WE ARE
   PROVIDED WITH THE DATA, STATISTICS, FIGURES...
   TO ASSESS, IF THE CLAIMS OF THE ARTICLE ARE
   SUPPORTED BY THE DATA.
   Only a small fraction of the manuscripts
   I come across provides
   this level of information. We should just
   start to turn down papers which do not
   back up their claims. We should not
   assume "that they probably got it right".

- As authors:
   WE SHOULD PROVIDE THE MATERIAL THE REVIEWERS
   NEED TO MAKE AN INFORMED JUDGEMENT ABOUT OUR
   STRUCTURE.
   We should submit extra figures and
   tables/ statistics. If we are doing a good
   job during structure analyis, you will have
   the data at hand anyway. We just tell the journal
   we do not expect all this extra stuff to be published,
   we just want to make sure that the reviewers
   can check our claim.
   I am sure the editors will not complain.

- As teachers/PI's
   TRAINING AND QUALITY CONTROL IN OUR OWN LABS
   IS THE FIRST LINE OF DEFENSE AGAINST
   BAD STRUCTURES.
   From looking at many of the
   questions (and answers) posted on this bulletin
   board, I get the impression that many students
   do not understand the basic principles
   of refinement or handle details of refinement
   and structure validation
   with a certain degree of laissez-faire.
   Worse, apparently many people have
   nobody in their own lab who can or is willing
   to answer their questions on such very basic
   issues.


-- 
Ulrich K. Genick
Assistant Professor
Department of Biochemistry
Brandeis University, MS009
Waltham, MA, 02454

Room   Kosow 108
Phone  781-736 2304
Fax    781-736 2349
Email  genick@brandeis.edu