Print

Print
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/