[ccp4bb] Procheck vs Molprobity

[Martin Hallberg]

I recently received a referee report that stated "The authors should  
describe the number of residues in the fully allowed, favored. The  
present statistic is misleading. Molprobity is far too loose (it even  
gives good values for structures that are wrong!) Procheck is more  
realistic."

That is basically the inverse of my own experience and there are some  
posts on the CCP4BB supporting this view (see for example http:// 
www.dl.ac.uk/list-archive-public/ccp4bb/2005-07/msg00227.html ). My  
first reaction was that the reviewer is simply not up to date. After  
checking a good number of recent papers, I find that almost all  
papers (of which some are by people active on this board) refer to  
the Procheck definition. Is this because Procheck is still  
distributed and supported by the CCP4?

The PDB has recently stopped displaying results from Procheck  
analysis under the geometry tab and now only gives a Molprobity plot.  
Perhaps it is time to re-think the inclusion of Procheck in further  
CCP4 distributions or at least put a note/warning about the Procheck  
Ramachandran in the relevant CCP4 documentation section?

Cheers,

Martin

PS. Quoting the Molprobity manual: "This new data shows a core region  
(98% of the data) that almost exactly matches the "strict" single  
region defined by Kleywegt & Jones (1996, Structure, 4, 1395), but it  
has in common with ProCheck (Laskowski et al., 1993, J. Appl.  
Crystallogr. 26, 283) the definition of an allowed outer region.  
However, it is now clear that the early ProCheck regions were too  
permissive in many places and missed the now-quite-distinct gamma- 
turn region near +70°, -60°."