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
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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