[phenixbb] question about composite SA_omit map in phenix

Pavel Afonine PAfonine at lbl.gov
Sun Aug 30 23:36:20 PDT 2009


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 <mailto:PAfonine at lbl.gov>
>     *To:* qunwan1 at gmail.com <mailto:qunwan1 at gmail.com> ; PHENIX user
>     mailing list <mailto:phenixbb at phenix-online.org>
>     *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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>
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