<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Zhenjiao,<div class=""><span class="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="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="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="Apple-tab-span" style="white-space:pre"> </span>from BuildStructure import placePeptide</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>from chimera import runCommand</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>placePeptide(<i class="">sequence</i><span style="font-style: normal;" class="">, [(</span><i class="">phi1</i><span style="font-style: normal;" class="">, </span><i class="">psi1</i><span style="font-style: normal;" class="">), (</span><i class="">phi2</i><span style="font-style: normal;" class="">, </span><i class="">psi2</i><span style="font-style: normal;" class="">), ... (</span><i class="">phiN</i><span style="font-style: normal;" class="">, </span><i class="">psiN</i><span style="font-style: normal;" class="">)])</span></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand("minimize <i class="">options-you-want</i>")</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand("write #0 <i class="">appropriate-file-name</i><span style="font-style: normal;" class="">")</span></div><div class=""><span class="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 style="font-style: normal;" class="">, </span><i class="">psi</i><span style="font-style: normal;" class="">)] * 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="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="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="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Good morning, Dear Professor,<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">My name is Zhenjiao Du, from Kansas State University.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">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.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">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.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">I am looking forward to your reply.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Sincerely,<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div class=""><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Zhenjiao Du<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Vice president of CAFS Student Committee</span><span style="" class=""><o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Ph.D. student, Cereal Chemistry<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Grain Science & Industry</span><span style="" class="">,<span class="Apple-converted-space"> </span></span><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Kansas State University</span><span style="" class=""><o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">150A Waters Hall</span><span style="" class="">,<span class="Apple-converted-space"> </span></span><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Manhattan, KS 66502<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class="">Pronouns: He/His</span><span style="" class=""><o:p class=""></o:p></span></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></span></div></div><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; 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