<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Zhenjiao,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I'm glad you got it to work. Have a great weekend!</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 7, 2022, at 2:26 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="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Good afternoon, Eric,</div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I am so grateful to your reply. I am so happy. That really make my day.<span id="🤩" class="">🤩<span id="🤩" class="">🤩<span id="🤩" class="">🤩<span id="🤩" class="">🤩<span id="😄" class="">😄<span id="😄" class="">😄<span id="😄" class="">😄<span id="😄" class="">😄<span id="😁" class="">😁<span id="😁" class="">😁<span id="😁" class="">😁</span></span></span></span></span></span></span></span></span></span></span></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">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="😄" class="">😄<span id="😄" class="">😄<span id="😄" class="">😄<span id="😄" class="">😄<span id="😄" class="">😄</span></span></span></span></span></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span class=""><span class=""><span class=""><span class=""><span class=""><br class=""></span></span></span></span></span></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span class=""><span class=""><span class=""><span class=""><span class="">Again, thank you so much for your reply, and the amazing software your team is working with. </span></span></span></span></span></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span class=""><span class=""><span class=""><span class=""><span class=""><br class=""></span></span></span></span></span></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">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><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Sincerely,<div class="">Zhenjiao</div></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div id="appendonsend" 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;" class=""></div><hr tabindex="-1" 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; display: inline-block; width: 501.75px;" class=""><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><div id="divRplyFwdMsg" dir="ltr" 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;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, October 8, 2022 2:26<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Zhenjiao Du <<a href="mailto:zhenjiao@ksu.edu" class="">zhenjiao@ksu.edu</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Enquiry about the ligand library generation by scripts in Chimera</font><div class=""> </div></div><div class="" 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; word-wrap: break-word; line-break: after-white-space;"><div style="width: 350px; margin: 0px auto; background-color: rgb(255, 255, 0); text-align: center;" class=""><div style="margin-top: 0px; margin-bottom: 0px; font-size: 15px; line-height: 28px; white-space: nowrap; font-weight: 700;" class="">This email originated from outside of K-State.</div></div><br class=""><div class="">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 class="Apple-converted-space"> </span></span><i class="">psi1</i><span class="" style="font-style: normal;">), (</span><i class="">phi2</i><span class="" style="font-style: normal;">,<span class="Apple-converted-space"> </span></span><i class="">psi2</i><span class="" style="font-style: normal;">), ... (</span><i class="">phiN</i><span class="" style="font-style: normal;">,<span class="Apple-converted-space"> </span></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<span class="Apple-converted-space"> </span><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 class="Apple-converted-space"> </span></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 class=""><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"><div class=""><div class="x_WordSection1" 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;"><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;">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=""></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="">,<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=""></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="">,<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><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;">Pronouns: He/His</span><span class=""></span></div></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;"> </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;"> </span></div></div><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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></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; text-decoration: none;" class=""><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="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><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; text-decoration: none;" class=""><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="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>