[phenixbb] Calculation of RSR for a fragment of PDB

[George Devaniranjan]

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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