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Thank you Pavel for your reply.
I cut out the density because I have many many fragments and NOT whole
protein structures.
For instance my fragments may go from 1-15, 2-18, 5-25, 6-28 …
So to compare my model for the same fragments I thought it was easier than
trying to fit the "modeled" fragment back into the whole protein.
For example if I modeled residues 10-25 in a 100 residue protein, I would
have to fir 1-9 from the native with 26-100 from the native to use the
un-cut density right?
Maybe I am wrong ? (likely given that I am just dipping my toes in this)
I do like your second suggestion, I will try that.
Thank you once again for your help.
George
On Mon, Jun 16, 2014 at 9:22 PM, Pavel Afonine
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