<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>The script I send is designed to be placed in a .py file and run directly (after you've created that trajectory of course). You run it simply by opening the .py file with the "open" command or File→Open. The script creates one file, with one line per frame indicting the helix percentage for that frame. It was meant as a jumping off point for writing whatever kind of analysis script you ultimately want.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Your modified version has a couple of misconceptions/problems. One is the "<FRAME>" is only defined within the MD Movie's dialog's Per-Frame scripting dialog, and only for Chimera-command scripts, not Python scripts (for Python scripts within that dialog it's "mdInfo['frame']"). The script I sent is not designed to run within the MD Movie dialog, so neither of those is relevant. If you really want one file per frame instead of a single combined file, you would need to move the open() (and close()) calls into the loop and base the file name off the 'i' variable.</div><div class=""><br class=""></div><div class="">--Eric</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 31, 2020, at 4:05 PM, 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="">Eric, </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="">Hey thank you so much for sending this over, t<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">his is a great little bit of code! </span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">If I were to want to run and save a new file per frame, how would I do that? I didn't put a ton of time into exploring it today, working on a code to loop through the files I got and show which helices are degrading first, but my initial attempts for the % helix code you sent over wouldn't write to individual files. Here is what I had tried. </span></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="">from chimera import runCommand as rc</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=""><span style="color: rgb(32, 31, 30); font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 15px; background-color: rgb(255, 255, 255); display: inline !important;" class="">from chimera import openModels, Molecule</span><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=""><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=""><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class="">outf = open("<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255); display: inline !important;" class="">r'path\to\output\<FRAME>helix.txt"</span>, "w")</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class="">m = openModels.list(modelTypes=[Molecule])[0]</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class="">for i, cs in enumerate(m.coordSets):</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""></span>m.activeCoordSet = cs</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""></span>numHelix = 0</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""></span>for r in m.residues:</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""></span>if r.isHelix:</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""></span>numHelix += 1</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""></span>print>>outf, "frame %d, %.1f%% helix" % (I, numHelix * 100.0 / len(m.residues))</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class="">outf.close()</div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);" class=""><br class=""></div>My issue on it is that the <FRAME> built in command from writesel did not translate into the python shell. When I tried to run my helix extraction to get the information about which helices were disappearing first I used:</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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">from chimera import runCommand as rc</span><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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">rc('ksdssp')</span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">rc('sel helix')</span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">rc('writesel (r'path\to\output\<FRAME>helix.txt')</span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></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="">but then this said that the <FRAME> (or maybe the writesel) command won't work in the python per script editor, so I used it in the chimera command per script piece and it worked great to get a new file per frame. </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 also played around with things like:</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="">#append list of % for all frames</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="">outf = open(<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">r'path\to\output\<FRAME>helix.txt','a')</span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">#wirte new file for each frame</span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">rc('writesel (r'path\to\output\%helix.txt')</span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">But that also did not work. </span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">Basically, I haven't been able to get the writing a new file per frame work in the the python shell yet. </span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">Thank you, </span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></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=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">Harrison </span></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 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: 487.046875px;" 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>Thursday, July 30, 2020 7:44 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Helmick, Harrison Dale Brent <<a href="mailto:hhelmick@purdue.edu" class="">hhelmick@purdue.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> <<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] Scripting Question</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;">Hi Harrison,<div class=""><span class="x_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="x_Apple-tab-span" style="white-space: pre;"></span>m.activeCoordSet = cs</div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>numHelix = 0</div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>for r in m.residues:</div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>if r.isHelix:</div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>numHelix += 1</div><div class=""><span class="x_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="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 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="x_Apple-interchange-newline"><div class=""><div class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">To the Chimera Team, </div><div class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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 class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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 class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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 class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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 class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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 class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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 class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="" 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; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">Thank you, </div><div 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;"><div class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div id="x_Signature" class=""><div class=""><div class=""></div><div id="x_divtagdefaultwrapper" dir="ltr" class="" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class=""></span>--</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Harrison Helmick</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" style="font-size: 11pt;">Graduate Research Assistant, Ross Fellowship</span></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" style="font-size: 11pt;">Kokini Lab, Purdue University</span></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" 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-weight: 400; text-decoration: none; word-spacing: 0px; white-space: normal; orphans: 2; float: none; background-color: transparent; display: inline !important;">Philip E. 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