[phenixbb] question about composite SA_omit map in phenix

Pavel Afonine PAfonine at lbl.gov
Fri Aug 28 09:31:41 PDT 2009

Hi Qun Wan,

Alternatively, you can ask phenix.refine to compute Average Kick Map, 
which is expected to be less biased or less noisy. For more details 
about kick map, see recent publication:

Acta Cryst. (2009). D65, 921-931.

Please let me know if you have questions.


On 8/28/09 7:52 AM, crystallogrphy wrote:
> Hi,
> I am using molecular replacement to build a model against a 2.2A 
> resolution data set. However, the template model only has 23% sequence 
> identity. First, I use chainsaw in CCP4i to prune all side chain to be 
> poly-Ala except the identical residues. Then I use AutoMR and rigid 
> body refinement, I got Rfree=50%. The continuous electron density is 
> not bad showing second structures. However, the model has some 
> out-of-registration problem, for example, two proline are in a 
> alpha-helix. In other words, it has model bias. I want to use 
> composite SA-omit to get a less model bias map, not a simple composite 
> omit map or a SA_omit map ommiting a part of the region.
> Does someone know who to do this?
> Thanks!
> Qun Wan
> postdoc fellow
> Case Western Reserve University
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