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Hi George,<br>
<br>
two lines to do this:<br>
<br>
phenix.get_cc_mtz_pdb cut_out_density.mtz modelledFragment.pdb<br>
phenix.get_cc_mtz_pdb cut_out_density.mtz nativeFragment.pdb<br>
<br>
or whatever the GUI clicks for this are.<br>
<br>
Please note, to rename cut_out_density.MTZ -> cut_out_density.mtz
, which is the bug on our side.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/16/14, 1:26 PM, George
Devaniranjan wrote:<br>
</div>
<blockquote
cite="mid:CAFU65PcmfMsXgWs0voL0Taheisk70qV1L4sKTTFD-bGwY1Wh+g@mail.gmail.com"
type="cite">
<div dir="ltr">Hi everyone,
<div><br>
</div>
<div>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.</div>
<div>
<br>
</div>
<div>I cut out a part of a map for a PDB fragment using phenix
map cut out density resulting in a MTZ file.</div>
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>how can I go about this? I tried using phenix.refine
couldn't get it to work.</div>
<div><br>
</div>
<div>I have attached the MTZ fragment, the original PDB fragment
and the modified PDB fragment.</div>
<div>native: nativeFragment.pdb</div>
<div>model: modelledFragment.pdb</div>
<div>MTZ: cut_out_density.MTZ</div>
<div><br>
</div>
<div>(I can see mine is worse but I want to quantify that
"badness")</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Thank you,</div>
<div>George</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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