[phenixbb] Calculation of RSR for a fragment of PDB

Pavel Afonine pafonine at lbl.gov
Wed Jun 18 12:08:55 PDT 2014

Hi George,

two lines to do this:

phenix.get_cc_mtz_pdb cut_out_density.mtz modelledFragment.pdb
phenix.get_cc_mtz_pdb cut_out_density.mtz nativeFragment.pdb

or whatever the GUI clicks for this are.

Please note, to rename cut_out_density.MTZ -> cut_out_density.mtz , 
which is the bug on our side.


On 6/16/14, 1:26 PM, George Devaniranjan wrote:
> 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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> phenixbb at phenix-online.org
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