<div dir="ltr">Thank you Pavel for your reply.<div><br></div><div>I cut out the density because I have many many fragments and NOT whole protein structures.</div><div>For instance my fragments may go from 1-15, 2-18, 5-25, 6-28 …</div>
<div>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.</div><div><br></div><div>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?</div>
<div>Maybe I am wrong ? (likely given that I am just dipping my toes in this)</div><div><br></div><div><br></div><div>I do like your second suggestion, I will try that.</div><div><br></div><div>Thank you once again for your help.</div>
<div>George</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 16, 2014 at 9:22 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">Hi George,<br>
<br>
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:<br>
<br>
phenix.real_space_correlation model_1.pdb data.mtz detail=residue<br>
phenix.real_space_correlation model_2.pdb data.mtz detail=residue<br>
<br>
You should be able to do the same using the GUI.<br>
<br>
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).<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everyone,<br>
<br>
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.<br>
<br>
I cut out a part of a map for a PDB fragment using phenix map cut out density resulting in a MTZ file.<br>
<br>
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).<br>
<br>
how can I go about this? I tried using phenix.refine couldn't get it to work.<br>
<br>
I have attached the MTZ fragment, the original PDB fragment and the modified PDB fragment.<br>
native: nativeFragment.pdb<br>
model: modelledFragment.pdb<br>
MTZ: cut_out_density.MTZ<br>
<br>
(I can see mine is worse but I want to quantify that "badness")<br>
<br>
Thank you,<br>
George<br>
</blockquote>
<br>
</div></div></blockquote></div><br></div>