Dear Careina,
Keep in mind that MolPrrobity does not see symmetry (unlike RefDens or
WHAT_CHECK). This means that the clashes that may come from having the wrong
spacegroup are not detected.
Good luck,
Robbie Joosten
> Date: Tue, 18 Jan 2011 10:52:48 +0100
> From: mjvanra...@cnb.csic.es
> Subject: Re: [ccp4bb] So many clashes
> To: CCP4BB@JISCMAIL.AC.UK
>
> - look at the clashes one by one and fix them, using your biochemical
> knowledge and common sense
> - make sure there are no mistakes in the protein sequence used (resequence if
> necessary), a few amino acids may be different from what you expect and,
> combined with local ambiguous density, lead to clashes
>
> Mark J van Raaij
> Laboratorio M-4
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3, Campus Cantoblanco
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.researcherid.com/rid/B-3678-2009
>
> On 18 Jan 2011, at 10:34, Careina Edgooms wrote:
>
> > Dear CCP4 bulletin board
> >
> > I am trying to solve structure with molecular-replacement. I have got good
> > solution using Phaser. The refined structure fits well toelectron density
> > and appears reasonable in terms of geometry, ramachandran, rotamers etc.
> > The problem I experience is that there are very many clashes and MolProbity
> > check gives a score of 34th percentile and when I refine, the Rfree does
> > not go below 30% for under 2A resolution. I tried reprocessing in different
> > space group (from P212121 to P21) and also got a MR solution. In P21 number
> > of clashes was reduced but still very high and Rfree was slightly reduced
> > but the gap between Rfree and R was still high. I am not sure what this
> > means and how I can sort out the problem of so many clashes? Any
> > suggestions would be helpful and appreciated
> >
> > regards
> > Careina
> >
> >
