<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 Harrison,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Elaine covered the writesel issue. Sounds like you are proficient with Python, so here's a short script that writes the percentage of residues that are helix each frame to a file:</div><div class=""><br class=""></div><div class="">outf = open("/Users/myself/location/helix_percent.txt", "w")</div><div class="">from chimera import openModels, Molecule</div><div class="">m = openModels.list(modelTypes=[Molecule])[0]</div><div class="">for i, cs in enumerate(m.coordSets):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>m.activeCoordSet = cs</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>numHelix = 0</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for r in m.residues:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>if r.isHelix:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>numHelix += 1</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>print>>outf, "frame %d, %.1f%% helix" % (I, numHelix * 100.0 / len(m.residues))</div><div class="">outf.close()</div><div class=""><br class=""></div><div class="">You can use Chimera's Python shell (Tools→General Controls→IDLE) to nose around, use dir() on things to find attributes, and to try things out. Feel free to ask more questions if needed.</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 Jul 30, 2020, at 10:07 AM, Helmick, Harrison Dale Brent <<a href="mailto:hhelmick@purdue.edu" class="">hhelmick@purdue.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">To the Chimera Team, </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">Hello, my name is Harrison Helmick, and I am a PhD student in Purdue University's department of food science. I hope that you all are doing well. </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">I am interested in developing more relationships between bioinformatic models and end use properties of foods, helping us understand and predict characteristics like emulsification, gelling, denaturation, etc. </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">I have been using Chimera to run molecular dynamic simulations, as well as analyze the protein structures and compare those to experimental properties. I'd like to see if there are predictable functional differences based on intermediate steps of denaturation of common seed storage proteins used in food. I have found Chimera to be super interesting and helpful in terms of my learning so far. </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">One of the characteristics I'd like to quantify is the change in secondary structure over the course of denaturation. I would like to have a script that returns the number of residues that are identified as the basic secondary structures so that I can graph the relative proportion of these structures of the course of the simulation. I'd also like to see which helices and strands are being degraded first, and I will compare that to their relative surface accessibility. </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">The way I have gone about this is to use the Chimera command per frame scripts KSDSSP, sel hex, and writesel to attempt to generate files for each frame. With a short python code, we could loop over the files to see which residue numbers disappear first and the progression of the destruction of helices, strands, etc. I haven't been able to get the dynamic file writing to work though, so I always write over the original file instead of saving it as a new one. </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">While I could probably figure out the dynamic file writing, this seems inefficient, and I was wondering if you all had a better script this process. </div><div 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, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div 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, Helvetica, sans-serif; font-size: 12pt;" class="">Thank you, </div><div 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 style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div class=""></div><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="" class=""></span>--</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Harrison Helmick</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 11pt;" class="">Graduate Research Assistant, Ross Fellowship</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 11pt;" class="">Kokini Lab, Purdue University</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="text-align: left; text-transform: none; text-indent: 0px; letter-spacing: normal; font-family: Calibri, sans-serif; font-size: 11pt; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; word-spacing: 0px; white-space: normal; orphans: 2; float: none; background-color: transparent; display: inline !important;" class="">Philip E. 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