If your dataextends to 2A resolution I suggest you run Arp-Warp or
Buccaneer to rebuild the structure. At that resolution the automated
building programd can usually fix errors.
At the end use this option to get the new build back to overlap the original
csymmatch -pdbin-ref MR.pdb -pdbin arp-sol.pdb
-pdbout arp-sol-overMR.pdb
Eleanor
On 01/18/2011 09:52 AM, Mark J van Raaij wrote:
- 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
