Martin Hallberg wrote:
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:// ). 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?

People know and are familiar with MolProbity.

I suggest you send the quote from the Molprobity manual back to the referees on this one. I would also cite its use by the PDB. You may also quote me if you like:

"The ProCheck Ramachandran plot data is based on old data, and it is my understanding that the software is no longer updated by the author. MolProbity by contrast includes new data from a large number of high resolution structures solved since the introduction of ProCheck and refined using more modern algorithms. In any disagreement between MolProbity and ProCheck, I would consider the MolProbity output to be authoritative. Kevin Cowtan, CCP4 bulletin board, February 2007"

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