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).

Pavel

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