[phenixbb] Calculation of RSR for a fragment of PDB

Pavel Afonine pafonine at lbl.gov
Mon Jun 16 18:22:30 PDT 2014

Hi George,

I'm not sure you need to carve out a box of density for what you are 
trying to do. Phenix tools that compute map CC can report it per residue 
(ligand). So you can just run it twice: with original and modified PDB 
files. A command line example would be:

phenix.real_space_correlation model_1.pdb data.mtz detail=residue
phenix.real_space_correlation model_2.pdb data.mtz detail=residue

You should be able to do the same using the GUI.

Alternatively, you can calculate one map using original model, then 
change the model (modify the ligand), and calculate second map, then use 
a tool that computes map CC from Fourier map coefficients and PDB file 
(phenix.get_cc_mtz_pdb or whatever the GUI equivalent is).


> Hi everyone,
> I apologize at the beginning itself as I am new to using PHENIX/X-ray 
> crystallography so this question might not make the most sense but I 
> will try and explain it well.
> I cut out a part of a map for a PDB fragment using phenix map cut out 
> density resulting in a MTZ file.
> Now I changed the fragment (changed its phi and psi externally) and 
> want to calculate the RSR [real-space R -factor] for the model based 
> on the old density (to check if I have made things worse or not).
> how can I go about this? I tried using phenix.refine couldn't get it 
> to work.
> I have attached the MTZ fragment, the original PDB fragment and the 
> modified PDB fragment.
> native: nativeFragment.pdb
> model: modelledFragment.pdb
> MTZ: cut_out_density.MTZ
> (I can see mine is worse but I want to quantify that "badness")
> Thank you,
> George

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