<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 Chimera support,<div class=""><br class=""></div><div class="">I want to extract a set of distances and one angle from each snapshot of an MD trajectory (there are 11 of them).</div><div class=""><div class="">My plan was to have all my distances appear in one of the MD-movie analysis>plot distances windows and use ‘Dump Values’ to get my numbers out in a way I could use for other plots.</div></div><div class="">I realize angles cannot appear in the same plot, but hope I can measure an angle in the same script.</div><div class=""><br class=""></div><div class="">I have a ‘per-frame’ script that runs fine on the first frame, however it returns ‘Problem in per-frame script: Distance monitor already exists’ when I step forward to a second frame.</div><div class=""><br class=""></div><div class="">Nothing appears in a 'MD plots' window (such a window does not open on its own either). </div><div class="">Reply Log shows the correct distances for the first frame but then only repeats the error after that.</div><div class=""><div class=""><font color="#ff2600" class="">Problem in per-frame script:</font></div><div class=""><font color="#ff2600" class="">Distance monitor already exists</font></div></div><div class=""><br class=""></div><div class=""><u class="">My work-flow</u>:</div><div class="">Open MD/movie, load my trajectory</div><div class="">open analysis, Per-Frame</div><div class="">copy my script into the window (chimera commands)</div><div class="">click ‘apply' in the script window, click ‘play’ or step forward one frame in the MD GUI (looping disabled)</div><div class=""><br class=""></div><div class=""><u class="">My scrip</u>t:</div><div class=""><div class="">~disp</div><div class="">~ribbon</div><div class="">disp :718,720,721,722,730,740,741,1058</div><div class="">distance :1058@O2 :741@ND1</div><div class="">distance :730@OH :741@NE2</div><div class="">distance :721@OG1 :1058@N5</div><div class="">distance :718@O :1058@N3</div><div class="">distance :721@N :1058@O4</div><div class="">distance :722@N :1058@O4</div><div class="">distance :720@N :1058@O4</div><div class="">distance :740@O :720@N</div><div class="">angle :1058@C2 :1058@O2 :741@HD1 :741@ND1</div></div><div class=""><br class=""></div><div class=""><u class="">Reply Log output</u>:</div><div class=""><div class="">Distance between FDM 1058 O2 and HID 741 ND1: 2.8</div><div class="">Distance between TYR 730 OH and HID 741 NE2: 2.8</div><div class="">Distance between THR 721 OG1 and FDM 1058 N5: 3.4</div><div class="">Distance between ILE 718 O and FDM 1058 N3: 3.2</div><div class="">Distance between THR 721 N and FDM 1058 O4: 2.9</div><div class="">Distance between GLY 722 N and FDM 1058 O4: 3.2</div><div class="">Distance between GLN 720 N and FDM 1058 O4: 3.2</div><div class="">Distance between GLN 740 O and GLN 720 N: 3.0</div><div class="">Dihedral #0:1058@C2 #0:1058@O2 #0:741@HD1 #0:741@ND1: -51.0515</div><div class="">Problem in per-frame script:</div><div class="">Distance monitor already exists</div><div class=""><br class=""></div></div><div class="">Thank you for any assistance,</div><div class="">Anne-Frances</div><div class=""><br class=""><div class="">
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-webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); 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; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); 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; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); 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; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); 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; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font color="#0000de" class="">- • - • - • - • - • - • - • - • -</font></div><div style="font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span style="font-style: normal;" class=""><b class=""><font color="#0000d2" class="">A.-F. Miller, Ph. D. (she/elle/sie)</font></b></span></div><font color="#0000d2" class="">University Research Professor<br class=""></font><div style="font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span style="font-style: normal;" class=""><font color="#0000d2" class="">Professor of Chemistry</font></span></div><span style="font-style: normal;" class=""><font color="#0000d2" class="">University of Kentucky</font></span></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="font-style: normal;" class=""><font color="#0000d2" class=""><a href="https://www.uky.edu/~afm/" class="">https://www.uky.edu/~afm/</a></font></span></div><div dir="auto" style="color: rgb(0, 0, 0); word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="color: rgb(0, 0, 0); font-style: normal;" class=""><font color="#0000de" class=""><br class=""></font></span><font color="#db0000" class="">Visiting Fellow, </font></div><div dir="auto" style="color: rgb(0, 0, 0); word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><font color="#db0000" class=""> Einstein Foundation of Berlin<br class=""></font></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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