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 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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Thanks, Pavel. This works. --Jianghai On Feb 28, 2013, at 1:26 PM, Pavel Afonine 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 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

---

phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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