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Eric, </div>
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Hey thank you so much for sending this over, t<span style="color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">his is a great little bit of code! </span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">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>
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from chimera import runCommand as rc</div>
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<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">from
chimera import openModels, Molecule</span><br>
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outf = open("<span style="color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255); display: inline !important">r'path\to\output\<FRAME>helix.txt"</span>, "w")</div>
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m = openModels.list(modelTypes=[Molecule])[0]</div>
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for i, cs in enumerate(m.coordSets):</div>
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<span style="margin: 0px"></span>m.activeCoordSet = cs</div>
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<span style="margin: 0px"></span>numHelix = 0</div>
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<span style="margin: 0px"></span>for r in m.residues:</div>
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<span style="margin: 0px"></span>if r.isHelix:</div>
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<span style="margin: 0px"></span>numHelix += 1</div>
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<span style="margin: 0px"></span>print>>outf, "frame %d, %.1f%% helix" % (I, numHelix * 100.0 / len(m.residues))</div>
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outf.close()</div>
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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>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">from chimera import runCommand as rc</span><br>
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</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">rc('ksdssp')</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">rc('sel helix')</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">rc('writesel (r'path\to\output\<FRAME>helix.txt')</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
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>
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I also played around with things like:</div>
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#append list of % for all frames</div>
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outf = open(<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">r'path\to\output\<FRAME>helix.txt','a')</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">#wirte new file for each frame</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">rc('writesel (r'path\to\output\%helix.txt')</span></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">But that also did not work. </span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">Basically, I haven't been able to get the writing a new file per frame work in the the python shell yet. </span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">Thank you, </span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><br>
</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">Harrison </span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, July 30, 2020 7:44 PM<br>
<b>To:</b> Helmick, Harrison Dale Brent <hhelmick@purdue.edu><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Scripting Question</font>
<div> </div>
</div>
<div class="" style="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><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">
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To the Chimera Team, </div>
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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>
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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>
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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>
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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>
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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>
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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>
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Thank you, </div>
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<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style=""></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. Nelson Hall of Food Science</span><br class="">
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<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; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; 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://plato.cgl.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; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div>
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