[phenixbb] Calculation of RSR for a fragment of PDB

George Devaniranjan devaniranjan at gmail.com
Tue Jun 17 05:38:11 PDT 2014

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.

On Mon, Jun 16, 2014 at 9:22 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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
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