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Hi Tom,</div>
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This is really a continuation of the markblobs conversation. <span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">The output of that creates markers with a new parent id, and all therefore all displayed at
once, but if I renamed the output to be a child of the frame it was initially marked on it showed the marker on the proper frame as I played through in time (and only at that time point). </span><span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">This
probably isn't the proper way, but it worked very quickly:</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">perframe "markblobs #1.$1; rename #2 centroid id #1.$1.2;" ranges 1,50</span></div>
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<img size="40698" contenttype="image/png" unselectable="on" tabindex="-1" style="max-width: 100%; user-select: none;" data-outlook-trace="F:1|T:1" src="cid:ad953a62-20d2-4851-962a-6645c5c44625"><br>
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The id_string is the desired id for the new markers. I added them when the first output cmm file is made to track in trackpy, and wrote the resulting tracks into a new cmm file, which I am trying to load into chimera as a child of the surface as you stated
below.</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(204, 204, 204); display: inline !important;">I'm
guessing that each of the marker sets in your file is tracking a single object in 3D light microscopy and the third digit (e.g 2 in 1.4.2) is an id number of that object.</span><br>
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<p><span style="color:rgb(0,37,84); font-size:18px; box-sizing:border-box; font-family:Arial,Helvetica,sans-serif"><span style="box-sizing:border-box; font-weight:bolder">Brandon Scott, PhD </span></span><span style="color:rgb(0,37,84); font-size:14px">CZI
Imaging Scientist, Research Assistant Professor</span><br>
</p>
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<strong style="box-sizing:border-box; font-weight:bolder; font-family:Arial,Helvetica,sans-serif">Nanoscience & Nanoengineering</strong></p>
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<span style="box-sizing:border-box; font-family:Arial,Helvetica,sans-serif">South Dakota Mines</span></p>
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<span style="box-sizing:border-box; font-family:Arial,Helvetica,sans-serif">501 E. Saint Joseph St., Rapid City, SD 57701</span></p>
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<span style="box-sizing:border-box; font-family:Arial,Helvetica,sans-serif">724.510.1253 |<span> </span><a href="mailto:Brandon.Scott@sdsmt.edu" style="box-sizing:border-box; color:rgb(56,94,157); background-color:rgba(0,0,0,0)">Brandon.Scott@sdsmt.edu</a></span></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Thursday, October 15, 2020 11:59 AM<br>
<b>To:</b> Scott, Brandon L. <Brandon.Scott@sdsmt.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [EXT] Re: [chimerax-users] Markers from CMM</font>
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<div>Hi Brandon,
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<div class=""> I don't understand your question in enough detail. Your attached cmm file has lines like:</div>
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<div class=""><marker_set name="track_1"></div>
<div class=""><marker id_string="1.4.2" id="1" frame="4" x="334.43" y="460.59" z="132" r="1" g="1" b="0" radius="0.5"/></div>
<div class=""><marker id_string="1.5.2" id="1" frame="5" x="335.47" y="461.79" z="123.72" r="1" g="1" b="0" radius="0.5"/></div>
<div class=""><marker id_string="1.6.2" id="1" frame="6" x="337.07" y="464.2" z="122.84" r="1" g="1" b="0" radius="0.5"/></div>
<div class="">...</div>
<div class="">
<div class=""><marker_set name="track_2"></div>
<div class=""><marker id_string="1.5.3" id="2" frame="5" x="45.584" y="338.65" z="94.399" r="1" g="1" b="0" radius="0.5"/></div>
<div class=""><marker id_string="1.6.3" id="2" frame="6" x="47.014" y="330.92" z="92.311" r="1" g="1" b="0" radius="0.5"/></div>
<div class=""><marker id_string="1.7.3" id="2" frame="7" x="41.197" y="318.39" z="93.004" r="1" g="1" b="0" radius="0.5"/></div>
</div>
<div class="">...</div>
<div class=""><br class="">
</div>
<div class="">Every marker has a different id_string. What do you intend the id_string to mean? Do you really mean that id_string is the model id? That would put each single marker in its own model. I see that the second digit (e.g. 4 in 1.4.2) corresponds
to your frame number. I'm guessing that each of the marker sets in your file is tracking a single object in 3D light microscopy and the third digit (e.g 2 in 1.4.2) is an id number of that object.</div>
<div class=""><br class="">
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<div class="">You also have id="1" for all markers in the first marker set named track_1. Every marker must have a different id, this id is the residue number and atom name for the marker. I guess you wrote this file using a script since ChimeraX would not
write a file where two markers have the same id.</div>
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<div class="">Your two perframe commands seem to be changing the model id numbers for 259 marker sets, maybe you are putting each as a submodel of the light microscopy time series images?</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<blockquote type="cite" class="">
<div class="">On Oct 14, 2020, at 7:51 PM, Scott, Brandon L. <<a href="mailto:Brandon.Scott@sdsmt.edu" class="">Brandon.Scott@sdsmt.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
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Hello all,</div>
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When loading markers from a cmm file (example attached), is there a way to specify which submodel the marker goes to rather than it creating a new id? I've added the id_string to the cmm file when I created a new one which is the desired model.</div>
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I hacked the following, which works, but there are hundreds of tracks so I would like to come up with an automated (and proper) way to do this.</div>
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perframe "rename #2.$1 track_1 id #1.$2.2;" ranges 1,113 ranges 4,116</div>
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perframe "rename #2.$1 track_2 id #1.$2.3;" ranges 114,259 ranges 5,150<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="color:rgb(0,37,84); font-size:18px; box-sizing:border-box; font-family:Arial,Helvetica,sans-serif"><span class="" style="box-sizing:border-box; font-weight:bolder">Brandon Scott,
PhD </span></span><span class="" style="color:rgb(0,37,84); font-size:14px">CZI Imaging Scientist, Research Assistant Professor</span><br class="">
</div>
<div class="" style="margin-top:0.5em; margin-bottom:0.5em; box-sizing:border-box; color:rgb(117,120,123); font-size:12px; background-color:rgb(255,255,255); line-height:1">
<strong class="" style="box-sizing:border-box; font-weight:bolder; font-family:Arial,Helvetica,sans-serif">Nanoscience & Nanoengineering</strong></div>
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<span class="" style="box-sizing:border-box; font-family:Arial,Helvetica,sans-serif">South Dakota Mines</span></div>
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<span class="" style="box-sizing:border-box; font-family:Arial,Helvetica,sans-serif">501 E. Saint Joseph St., Rapid City, SD 57701</span></div>
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<span class="" style="box-sizing:border-box; font-family:Arial,Helvetica,sans-serif">724.510.1253 |<span class=""> </span><a href="mailto:Brandon.Scott@sdsmt.edu" class="" style="box-sizing:border-box; color:rgb(56,94,157); background-color:rgba(0,0,0,0)">Brandon.Scott@sdsmt.edu</a></span></div>
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<span id="x_cid:39DA9E67-DE87-4AF4-AAF0-5935C09F346C"><Cells_trackedV2.cmm></span><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">_______________________________________________</span><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">ChimeraX-users
mailing list</span><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">
<a href="mailto:ChimeraX-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">ChimeraX-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">
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subscription:</span><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">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-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://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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