[phenixbb] Calculation of RSR for a fragment of PDB

[George Devaniranjan]

Thank you- Edward Berry's and your steps should help me on  my way.

Thank you so much for putting up with this novice's questions !
i appreciate all the help I have got in this community.


On Wed, Jun 18, 2014 at 3:08 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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.
>
> Pavel
>
>
> 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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>
>
>
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