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<div>Dear Mengbin,</div>
<div>You can open a terminal window and run elbow as a command line.</div>
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<pre>phenix.elbow --final_geometry input_file.pdb<o:p></o:p></pre>
<!--EndFragment--></div>
<div><br>
</div>
<div>Do not forget to initialize the phenix environment, depending on your terminal shell, one example is:</div>
<div><span class="Apple-style-span" style="font-family: Cambria; font-size: 16px; ">source /Applications/PHENIX-dev-1320/Contents/phenix-dev-1320/phenix_env.sh</span></div>
<div><br>
</div>
<div>All the best,</div>
<div>Joao</div>
<div><br>
</div>
<div>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">Dr Joao Dias</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">Principal Scientist<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; "><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">Heptares Therapeutics Ltd</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">BioPark, Broadwater Road,</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">Welwyn Garden City,</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">Herts, AL7 3AX</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; color: black; margin-top: 0cm; margin-bottom: 0.0001pt; ">
<span style="font-size: 10pt; font-family: Arial, sans-serif; ">UK</span></p>
</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>Mengbin Chen <<a href="mailto:mengbinc@sas.upenn.edu">mengbinc@sas.upenn.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 13 June 2013 19:32<br>
<span style="font-weight:bold">To: </span>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
<span style="font-weight:bold">Subject: </span>[phenixbb] elbow<br>
</div>
<div><br>
</div>
<div>
<div>
<div dir="ltr">Dear PHENIX Users,
<div><br>
</div>
<div>I have been playing around with Elbow for a while, but I kept having problems generating .cif file. For "Chemical file type" and "Template PDB file", I used the pdb file of the ligand. Since the coordinates in the pdb file corresponds to a conformation
desired, I chose "None" for "geometry optimization". After running Elbow, the output pdb file was completely different than the input one -- even double bonds became single bonds and 10-membered ring conformation changed. I have tried Sketcher in CCP4 package,
but no good results either. Could anyone tell me how to do this correctly? Any help is appreciated!</div>
<div><br>
</div>
<div>Thank you in advance,</div>
<div>Mengbin<br clear="all">
<div><br>
</div>
-- <br>
Mengbin Chen
<div>Department of Chemistry</div>
<div>University of Pennsylvania</div>
</div>
</div>
</div>
</div>
</span><br>
<p></p>
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<p><a href="www.heptares.com" target=""><img border="0" width="650" height="65" src="cid:6827ea.png@23f44ab5.4ab0cb04" alt="www.heptares.com"></a><a href="http://www.heptares.com"></a></p>
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<td> </td>
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<font color="#595959" size="2" face="Calibri">The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have
received this transmission in error, please make no use of its contents and contact the sender. Contact and registered office address: Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX. Company No: 06267989</font></p>
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