[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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