Not sure if in any of the 112 posts regarding either the retraction
theme or 'was 12 retraction' theme did mention, that after all despite
good or as good as possible refinement of the structure, the goal is
still to describe as accurately as possible the biological system
using crystallography as a tool.
If you can't confirm your structure by solid biochemical or
biophysical methods what conclusions should you draw ?
Sure faking data is not the default and looking at the ratio of
suspected faked structures / deposited structures I do believe we are
doing much better than other researchers e.g. in medical science.
I agree that validation tools are very helpful and everybody should
use them prior to deposition of your structure to ensure good
standards and if you are not happy with the result of those validation
tools e.g. Procheck, Molprobity well then change something - re-refine
your structure and fix it prior to deposition.
Regarding paper submissions, I think it would be a good idea to
include e.g. the Molprobity Ramachandran plot & the summary attached
to the cover letter when submitting - additional to the table 1 of
course. Bill Scott once mentioned that he provides a Pymol scene file
with PDB coordinates & electron density map to reviewers, if one could
ensure that the coordinates can not be extracted from this file, I
would be willing to do the same, but it's to easy to extract the
coordinates and save them for 'other purposes'.
My 2.5 cents,
Jürgen
On Dec 13, 2009, at 1:35 PM, Nicholas M Glykos wrote:
Those Greeks again ...
Finally, validation tools are not there to pass judgement. They are
tools to be used by depositors, referees, and users alike, to help
them
make a better informed interpretation of crystallographic *models*.
Servers like EDS and PDB_REDO must be seen in that light,
Validation tools are programs written by crystallographers and
structural
biologists. As it happens, most crystallographers that write programs,
have the neurotic belief that they can treat others' people data
better
than those other people. And, I share that neurosis ;-))
--
Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
+302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
