- 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 > >
