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Good afternoon, Eric,</div>
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I am so grateful to your reply. I am so happy. That really make my day.<span id="🤩">🤩<span id="🤩">🤩<span id="🤩">🤩<span id="🤩">🤩<span id="😄">😄<span id="😄">😄<span id="😄">😄<span id="😄">😄<span id="😁">😁<span id="😁">😁<span id="😁">😁</span></span></span></span></span></span></span></span></span></span></span></div>
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Based on your suggestions, I successfully built an automatic workflow for peptide ligand generation by combining the available function and PyAutoGUI. It is a little bit stupid approach to implement my job, but finally it works out. <span id="😄">😄<span id="😄">😄<span id="😄">😄<span id="😄">😄<span id="😄">😄</span></span></span></span></span></div>
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<span><span><span><span><span><br>
</span></span></span></span></span></div>
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<span><span><span><span><span>Again, thank you so much for your reply, and the amazing software your team is working with. </span></span></span></span></span></div>
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<span><span><span><span><span><br>
</span></span></span></span></span></div>
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I hope I can go deeper into the molecular docking and dynamics simulation world. One day, I can have the opportunity to study and work at UCSF.</div>
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Sincerely,
<div>Zhenjiao</div>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Saturday, October 8, 2022 2:26<br>
<b>To:</b> Zhenjiao Du <zhenjiao@ksu.edu><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Enquiry about the ligand library generation by scripts in Chimera</font>
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<p style="font-size:15px; line-height:28px; color:black; white-space:nowrap; font-weight:700">
This email originated from outside of K-State.</p>
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<div>Hi Zhenjiao,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>You need to resort to Python to do this since there is no command equivalent for peptide building. I don't know how familiar you are with Python programming, but there is some basic
information for using Python in Chimera here: <a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html" class="">Chimera Programmer's Guide</a>.</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Specifically you would use the BuildStructure.placePeptide() function to construct the peptide ligand(s) and just run the "minimize" command to minimize them. You can run Chimera commands
from Python using the runCommand() function as described here: <a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">Very Basic Chimera Programming Primer</a>.</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>You would need to write a loop that goes through your peptide sequences (and possibly associated phi/psis). The inside of the loop would have some code similar to:</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>from BuildStructure import placePeptide</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>from chimera import runCommand</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>placePeptide(<i class="">sequence</i><span class="" style="font-style:normal">, [(</span><i class="">phi1</i><span class="" style="font-style:normal">,
</span><i class="">psi1</i><span class="" style="font-style:normal">), (</span><i class="">phi2</i><span class="" style="font-style:normal">,
</span><i class="">psi2</i><span class="" style="font-style:normal">), ... (</span><i class="">phiN</i><span class="" style="font-style:normal">,
</span><i class="">psiN</i><span class="" style="font-style:normal">)])</span></div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>runCommand("minimize
<i class="">options-you-want</i>")</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>runCommand("write #0 <i class="">appropriate-file-name</i><span class="" style="font-style:normal">")</span></div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>runCommand("close all")</div>
<div class=""><br class="">
</div>
<div class="">Tip, if you want all the residues to start with the same phi/psis, the second argument to placePeptide() could be: [(<i class="">phi</i><span class="" style="font-style:normal">,
</span><i class="">psi</i><span class="" style="font-style:normal">)] * len(</span><i class="">sequence)</i></div>
<div class=""><br class="">
</div>
<div class="">
<div class="">--Eric</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Oct 6, 2022, at 8:27 PM, Zhenjiao Du via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
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<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Good morning, Dear Professor,</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">My name is Zhenjiao Du, from Kansas State University.</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular
dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job.</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate
thousands of peptide ligands for virtual screening. I find Chimera also supports python programming.</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it.</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">I am looking forward to your reply.</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Sincerely,</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
<div class="">
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Zhenjiao Du</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Vice president of CAFS Student Committee</span><span class="" style=""></span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Ph.D. student, Cereal Chemistry</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Grain Science & Industry</span><span class="" style="">,<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Kansas
State University</span><span class="" style=""></span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">150A Waters Hall</span><span class="" style="">,<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Manhattan,
KS 66502</span></div>
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<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt; font-family:"Times New Roman",serif">Pronouns: He/His</span><span class="" style=""></span></div>
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<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
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<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
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<span class="" style="font-size:12pt; font-family:"Times New Roman",serif"> </span></div>
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Chimera-users
mailing list:<span class="x_Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Manage
subscription:<span class="x_Apple-converted-space"> </span></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a></div>
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