Hi Ulrich,

in your parameter file just add another map scope to the electron_density_maps scope, like this:

  electron_density_maps {
    map {
      mtz_label_amplitudes = "2FOFCWT_kick"
      mtz_label_phases = "PH2FOFCWT_kick"
      likelihood_weighted = True
      obs_factor = 2
      calc_factor = 1
      kicked = True
      fill_missing_f_obs_with_weighted_f_model = False
    }
    map {
      mtz_label_amplitudes = "FOFCWT_kick"
      mtz_label_phases = "PHFOFCWT_kick"
      likelihood_weighted = True
      obs_factor = 1
      calc_factor = 1
      kicked = True
      fill_missing_f_obs_with_weighted_f_model = False
    }
}

This will create two additional kick maps in addition to the default maps.

Pavel.



On 8/28/09 9:53 AM, Ulrich Baumann wrote:
Pavel, how can I specify the request for averaged Kick Maps on the command line , please?
 
Cheers,
Uli
----- Original Message -----
From: Pavel Afonine
To: [email protected] ; PHENIX user mailing list
Sent: Friday, August 28, 2009 6:31 PM
Subject: Re: [phenixbb] question about composite SA_omit map in phenix

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.

Pavel.


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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