[phenixbb] text output for model quality and validation report at phenix

Pavel Afonine PAfonine at lbl.gov
Mon Jan 4 11:28:53 PST 2010

Hi Ravi,

to get a plain text list of map CC computed per residue or per each atom 
you can use one of these two command line tools:

phenix.model_vs_data model.pdb data.hkl

or (if you want to have more options and flexibility), type:


hit Enter, and then follow the instructions.

Note, in both options, in addition to getting map CC you will also get 
2mFo-DFc and mFo-DFc printed for each atom or residue. These are very 
useful map quality measures that are complimentary to map CC. Example: 
sometime even a very weak density, say at sigma 0.1, can produce a high 
map CC, and if you just look at map CC you will miss it. So, I believe 
it is useful to look at triplets (CC, 2mFo-DFc, mFo-DFc) for each atom 
or residue, and this is what the above tools give you.
Of course, you get it from GUI as well.


On 1/4/10 10:46 AM, Ravindra D. Makde wrote:
> Hi all,
> I will greatly appreciate the answers to following query:
> How can  I get the text or excel output of the model quality and 
> validation report  of a model after phenix refinement? 
> I am specially interested in real space CC of the various residues. 
> I am  using phenix.refine_gui  at phenix-1.4-162. I have searched all 
> output files, but couldn't find.
> Thanks in advance.
> Ravi

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