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
