On 10 Sep 2009, at 19:29, Pavel Afonine wrote:
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:
If resolution allows, eg better than 2.5 A, good old ARP/wARP will do
the trick as well, if the solution is correct.
More details:
http://www.ncbi.nlm.nih.gov/pubmed/18094467?ordinalpos=13&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
Tassos
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:
<ATT00001.jpg>
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
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