[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

New structure validation program DDQ

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Dear all,

I would like to bring your attention to a new crystal structure 
validation program called DDQ that has appeared in Acta D this year 
(Jan 1999 issue). This program is different from other validation 
programs in that it quantifies a signature of correctly and completely
refined crystal structures and that is: very strong and correctly 
positioned positive water peaks in a hydrated difference map (i.e. 
waters deliberately removed from map calculation) and absence of shift 
peaks and UFO peaks (due to unmodeled residues, ligands, etc.). 
The latter is unfortunately a forgotten but important aspect in  
validating structures (because a partial correct structure is still 
partially incorrect by omission). To determine when a structure is 
refined to completion in reciprocal space is hard to assess just 
using the R and Rfree but DDQ attempts to assess that in real space.

DDQ has been tested thoroughly on >100 structures and could easily
detect 10 unnoticed errors in a published 2.4 Ang structure (R<20%) 
with no false positives (including a peptide flip, frame shift etc.)
as well as errors in high resolution structures (see 
van den Akker & Hol (1999) Acta D55: 206-218).

DDQ combines both global accuracy (i.e. low phase error --> strong
water peaks) with local accuracy (correctly positioned water peaks, no 
shift peaks) to arrive at local and global quality indicators which 
are then ranked against structures from the PDB (in a resolution bin 
dependent fashion) to facilitate a direct comparison with other 
structures. The DDQ program can also aid in speeding up refinement 
and also be used as a quantitative difference map quality indicator 
(for example, when you need to play with different scales or 
resolution ranges etc.).

For more information, to obtain an electronic color version of the 
Acta D paper described DDQ, or to download the DDQ program visit:

The DDQ program (F77) is free for both academic and commercial users.

Dr. F. van den Akker
Department of Molecular Biology/NB-20 
Cleveland Clinic Foundation
Lerner Research Institute
9500 Euclid Av.
Cleveland OH 44195                     e-mail: focco@pierre.lerner.ccf.org