[phenixbb] real_space_correlation

Jianghai Zhu jzhu at idi.harvard.edu
Thu Feb 28 12:37:37 PST 2013


Thanks, Pavel.  This works.

--Jianghai

On Feb 28, 2013, at 1:26 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Jianghai,
> 
> you will need to calculate this map fist and then use
>   phenix.get_cc_mtz_pdb model.pdb map_coeffs.mtz
> to get your CC.
> 
> Pavel
> 
> On 2/28/13 10:11 AM, Jianghai Zhu wrote:
>> Hi Pavel,
>> 
>> Is there a way in phenix to do what I wanted, i.e. calculate the real space cc between a model and a SA omit map?  Thanks.
>> 
>> --Jianghai
>> 
>> 
>> 
>> On Feb 28, 2013, at 12:56 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> 
>>> Hi Jianghai,
>>> 
>>> when you run
>>> 
>>>    phenix.real_space_correlation m.pdb d.mtz
>>> 
>>> it will calculate and output map correlation coefficients (map CC) between two maps: map_1=Fmodel map and map_2=2mFo-DFmodel, where Fmodel = k_total * (Fcalc + Fbulk), and 2mFo-DFmodel is what's called sigmaa map. These maps are calculated using the model from input PDB file, and reflection data (Fobs or Iobs) and R-free-flags from input reflection file.
>>> 
>>> You can define map_1 and map_2.
>>> 
>>> Depending on data resolution, the map CC will be reported per individual atom or per entire residue.
>>> 
>>> Pavel
>>> 
>>> On 2/27/13 1:17 PM, Jianghai Zhu wrote:
>>>> Hi All,
>>>> 
>>>> I was trying to use "phenix.real_space_correlation *.pdb resolve_composite_map.mtz" to get some real space cc for my ligand against the SA composite omit map.  But I am not sure that the map used here was the SA composite omit map.  Will phenix use the omit map I provided or will it just simply calculate a sigmaA weighted 2Fo-Fc map based on the pdb?
>>>> 
>>>> Thanks.
>>>> 
>>>> --Jianghai
>>>> 
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