- 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
>
>
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