<div dir="ltr">Thank you- Edward Berry's and your steps should help me on my way.<div><br></div><div>Thank you so much for putting up with this novice's questions !</div><div>i appreciate all the help I have got in this community.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jun 18, 2014 at 3:08 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
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<div><div class="h5"><br>
<br>
<div>On 6/16/14, 1:26 PM, George
Devaniranjan wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<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></fieldset>
<br>
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</blockquote>
<br>
</div>
</blockquote></div><br></div>