<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="">Hi Samo,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Strictly speaking, the answer is no. However, you can call the Python function that Surfnet uses with some simple Python code, namely:</div><div class=""><br class=""></div><div class="">from Surfnet import interface_surfnet</div><div class="">Interface_surfnet("#0", "#0")</div><div class=""><br class=""></div><div class="">This assumes you want to run Surfnet on all of model #0. You can use different atom specs in the second line above if you want to do something different than that.</div><div class=""><br class=""></div><div class="">Anyway, you can put those two lines in the MD Movie's Per Frame→define script dialog ("Interpret script as Python" in the resulting dialog), or put them in a file ending with .py and open that .py file every trajectory frame (again, probably with the "define script" dialog).</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 class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 31, 2022, at 12:49 AM, Samo Lešnik via Chimera-dev <<a href="mailto:chimera-dev@cgl.ucsf.edu" class="">chimera-dev@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" 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-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear Madam/Sir,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I was wondering if it is possible to run the Surfnet calculation using the command line tool. I wish to automate it for MD trajectory for every frame and this would be useful.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you!</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Samo</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""><font size="3" face="Calibri,Helvetica,sans-serif" style="font-family: Calibri, Helvetica, sans-serif, serif, EmojiFont;" class=""><span id="divtagdefaultwrapper" style="font-size: 12pt;" class=""><font size="3" face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" class=""><span id="divtagdefaultwrapper" style="font-size: 12pt;" class=""></span></font></span></font></p><font size="3" face="Calibri,Helvetica,sans-serif" style="font-family: Calibri, Helvetica, sans-serif, serif, EmojiFont;" class=""><font size="3" face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" class=""><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="de" style="font-size: 8pt;" class="">Dr. Samo Lešnik, mag. farm. /<span class="Apple-converted-space"> </span></span></font><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span style="font-size: 8pt;" class="">Researcher</span></font><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span style="font-size: 8pt;" class=""><br class=""></span></font></div><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="en-US" style="font-size: 8pt;" class="">Univerza v Mariboru / University of Maribor</span></font></div><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="en-US" style="font-size: 8pt;" class=""><b class="">Fakulteta za kemijo in kemijsko tehnolgijo</b></span></font></div><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="en-US" style="font-size: 8pt;" class=""><b class="">Faculty of Chemistry and Chemical Engineering</b></span></font></div><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="en-US" style="font-size: 8pt;" class="">Smetanova ulica 17, 2000 Maribor, Slovenija</span></font></div><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="en-US" style="font-size: 8pt;" class="">T: +386 2 2294 428</span></font></div><div style="margin: 0px;" class=""><font size="1" face="Calibri,sans-serif,serif,EmojiFont" color="#006A8E" class=""><span lang="en-US" style="font-size: 8pt;" class="">E:<span class="Apple-converted-space"> </span><a href="mailto:samo.lesnik@um.si" class="OWAAutoLink" id="LPNoLP">samo.lesnik@um.si</a></span></font></div></font></font><br class=""><p style="margin-top: 0px; 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