Hi Careina, Are you using riding hydrogens during refinement? The default in Refmac is to use hydrogens only if present in the input file - change this setting under the "Refinement Parameters" to "generate all hydrogens". This significantly helps with clashes.
Also, did you check the quality of your molecular replacement input model? If this model had a lot of clashes, then you are starting with the same problems and it can be difficult to overcome. At better than 2 ang. resolution, one of the automated building programs (arp/warp, resolve, buccaneer, ...) should be able to rebuild much of your model and may help with your clash problem too. good luck, Eric ================================ Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu ================================ On Tue, 18 Jan 2011, 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 to electron 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
