<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Dear Dr. </span><span style="font-size:13px;font-family:Arial,sans-serif">Dias,</span><div style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:Arial,sans-serif"><br>
</span></div><div style="font-family:arial,sans-serif;font-size:13px"><font face="Arial, sans-serif">I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation.</font></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font face="Arial, sans-serif"><br></font></div><div style="font-family:arial,sans-serif;font-size:13px"><font face="Arial, sans-serif">Thank you,</font></div><div style="font-family:arial,sans-serif;font-size:13px">
<font face="Arial, sans-serif">Mengbin</font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 13, 2013 at 2:52 PM, Mengbin Chen <span dir="ltr"><<a href="mailto:mengbinc@sas.upenn.edu" target="_blank">mengbinc@sas.upenn.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Dr. <span style="font-family:Arial,sans-serif;font-size:13px">Dias,</span><div><span style="font-family:Arial,sans-serif;font-size:13px"><br>
</span></div><div><font face="Arial, sans-serif">I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation.</font></div>
<div><font face="Arial, sans-serif"><br></font></div><div><font face="Arial, sans-serif">Thank you,</font></div><div><font face="Arial, sans-serif">Mengbin</font></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra">
<br>
<br><div class="gmail_quote">On Thu, Jun 13, 2013 at 2:42 PM, Joao Dias <span dir="ltr"><<a href="mailto:joao.dias@heptares.com" target="_blank">joao.dias@heptares.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Dear Mengbin,</div>
<div>You can open a terminal window and run elbow as a command line.</div>
<div>
<pre>phenix.elbow --final_geometry input_file.pdb<u></u><u></u></pre>
</div>
<div><br>
</div>
<div>Do not forget to initialize the phenix environment, depending on your terminal shell, one example is:</div>
<div><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>
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<span style="font-size:10pt;font-family:Arial,sans-serif">Dr Joao Dias</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></p>
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<span style="font-size:10pt;font-family:Arial,sans-serif">Principal Scientist<u></u><u></u></span></p>
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<span style="font-size:10pt;font-family:Arial,sans-serif">Heptares Therapeutics Ltd</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></p>
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<span style="font-size:10pt;font-family:Arial,sans-serif">BioPark, Broadwater Road,</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></p>
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<span style="font-size:10pt;font-family:Arial,sans-serif">Welwyn Garden City,</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></p>
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<span style="font-size:10pt;font-family:Arial,sans-serif">Herts, AL7 3AX</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></p>
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<span style="font-size:10pt;font-family:Arial,sans-serif">UK</span></p>
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<span style="font-weight:bold">From: </span>Mengbin Chen <<a href="mailto:mengbinc@sas.upenn.edu" target="_blank">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" target="_blank">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" target="_blank">phenixbb@phenix-online.org</a>><br>
<span style="font-weight:bold">Subject: </span>[phenixbb] elbow<br>
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<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>
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<font color="#595959" 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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</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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</div></div></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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