Hi Sylvia,

although modern MR programs perform rigid body refinement, it may be worth of giving a try a novel rigid body refinement protocol implemented in phenix.refine (MZ rigid-body refinement protocol), that has very high convergence radius:
J. Appl. Cryst. (2009). 42, 607-615. "Automatic multiple-zone rigid-body refinement with a large convergence radius".

Next step would be to try torsion angle (or Cartesian) simulated annealing refinement. You can also try combining it with real-space refinement. More details: 

Please let me know if you have questions about the above options, or/and: http://www.phenix-online.org/

Pavel.



On 9/10/09 9:05 AM, Sylvia Fanucchi wrote:

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Hi everyone

 

I am new to solving crystal structures so apologies for the simple question

 

I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial value was 0.49 (after 20 cycles of rigid body refinement). After analysing the output and a further 20 cycles of refinement, the R-factor is now 0.48. I would like to know if it is ever worthwhile to continue refining a structure when the initial R factors are so high? If so, what could I do to improve the refinement? 

 

Thanks for your suggestions

 

Best regards

Sylvia Fanucchi Ph.D

Protein Structure-Function Research Unit
East Campus, Gate House Room 416
School of Molecular and Cell Biology
University of the Witwatersrand
Johannesburg 2050
South Africa

Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 
E-mail: [log in to unmask] 

 

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