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This brings me a related issue with COOT: the spherical refinement does not consider symeqs either or does it? Xavier -------- 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