<div dir="ltr">Got it, thanks Phil!<div><br></div><div style>Mengbin Chen</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, May 21, 2013 at 4:22 PM, Jeffrey, Philip D. <span dir="ltr"><<a href="mailto:pjeffrey@princeton.edu" target="_blank">pjeffrey@princeton.edu</a>></span> wrote:<br>
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<div style="direction:ltr;font-size:10pt;font-family:Tahoma">In the section that looks like this in the header of the PDB file out of phenix.refine:
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<div>REMARK � 3 �DEVIATIONS FROM IDEAL VALUES.</div>
<div>REMARK � 3 � � � � � � � � RMSD � � MAX �COUNT</div>
<div>REMARK � 3 � BOND � � �: �0.002 � 0.058 � 6768</div>
<div>REMARK � 3 � ANGLE � � : �0.634 � 9.630 � 9127</div>
<div>REMARK � 3 � CHIRALITY : �0.046 � 0.300 � 1037</div>
<div>REMARK � 3 � PLANARITY : �0.003 � 0.040 � 1182</div>
<div>REMARK � 3 � DIHEDRAL �: 13.422 �88.272 � 2558</div>
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<div>The bottom line is that the PDB file out of refinement contains much of the info you will need for the refinement section of PDB deposition.</div>
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<div>Phil Jeffrey�</div>
<div>Princeton</div>
<div style="font-size:16px;font-family:Times New Roman">
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<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] on behalf of Mengbin Chen [<a href="mailto:mengbinc@sas.upenn.edu" target="_blank">mengbinc@sas.upenn.edu</a>]<br>
<b>Sent:</b> Tuesday, May 21, 2013 4:15 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] depositing pdb files<br>
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<div dir="ltr">I see, thanks a lot! Also, where can I get the rmsd dihedral angle value?
<div><br>
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<div>Thanks again,
<div>Mengbin</div>
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<div class="gmail_extra"><br>
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<div class="gmail_quote">On Tue, May 21, 2013 at 3:56 PM, Ed Pozharski <span dir="ltr">
<<a href="mailto:epozh001@umaryland.edu" target="_blank">epozh001@umaryland.edu</a>></span> wrote:<br>
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<div>Just do not report luzzati errors, they are essentially meaningless.� PDB is not going to reject your deposition because of that.
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<br>
On 05/21/2013 03:15 PM, Mengbin Chen wrote:<br>
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<div dir="ltr">Hi Phenix Users,
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<div>I am going to deposit some pdb files into RCSB, which requires Luzzati plots and a bunch of other things. I don't know how to get these results from Phenix (actually the main problem is luzzati errors, Phenix does not seem to provide them), although SFcheck
from CCP4i provides only some of them. I know CNS can do this by model_stats.inp, but that's too much trouble since I have complicated ligands bound. �Any suggestions would be appreciated!</div>
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<div>Thank you in advance,</div>
<div>Mengbin<br clear="all">
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-- <br>
Mengbin Chen
<div>Department of Chemistry</div>
<div>University of Pennsylvania</div>
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<br>
<pre cols="72">--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
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-- <br>
Mengbin Chen
<div>Department of Chemistry</div>
<div>University of Pennsylvania</div>
</div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Mengbin Chen<div>Department of Chemistry</div><div>University of Pennsylvania</div>
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