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
>>
>>
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