[phenixbb] on the criteria for outliers, phenix.molprobity and wwPDB validation

[Jorge Iulek]

Hi all,


	I had already noticed that outliers spotted by phenix with its 
validation tool, with the nice feature to carry one straight to the 
"suspicious" residue in a coot session for visual inspection, differs a 
bit from what comes spotted from wwPDB validation, generally the latter 
spotting some few more residues.
	To one current structure, which at low resolution, I notice there is a 
bit larger difference between the number of spotted residues.
	I see from wwPDB validation, molprobity is also used to spot  outliers 
for many of the analyses. I see the current molprobity version used is 
4.02b-467, but I could not yet devise the molprobity version used by 
phenix. Of course, there would also be the "library" used in each case 
to spot the outliers. Maybe someone ever listed what is considered in 
each case, and their differences, or a link to that is welcome for me.
	What would be the best criteria for spotting is of course a good 
discussion. But a superficial question I would make is if there is a way 
to make phenix.molprobity output to resemble the one from wwPDB 
validation, at least the ones accounted by molprobity?

Jorge