-------- Original Message --------

Subject:	Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
Date:	Thu, 23 Oct 2014 14:53:53 +0200
From:	Jose Manuel Duarte <[log in to unmask]>
Reply-To:	Jose Manuel Duarte <[log in to unmask]>
To:	[log in to unmask]

Molprobity does not look at contacts from symmetry partners, but only at 
the asymmetric unit ones.

Unfortunately the clash scores in the PDB validation reports are based 
on Molprobity and thus they won't count clashes outside the AU. See for 
instance structures 4bmw or 1jkm. Both contain serious clashes in 
symmetry-related partners but the clash scores for them are not showing 
that at all.

If one downloads the full validation report from the PDB, it is then 
possible to get information on non-AU clashes as well, calculated with 
Validation-pack. See this document 
http://wwpdb.org/ValidationPDFNotes.html for a detailed explanation.

Cheers

Jose



On 23/10/14 12:43, Tim wrote:
> Hi everybody,
> Molprobity does not take into account contacts/clashes from 
> symmetry-related molecules, or does it?
> Thanks in advance,
> Tim