[chimerax-users] [EXT] Re: Markers from CMM

[Scott, Brandon L.]

Hi Tom,

This is really a continuation of the markblobs conversation. 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). This probably isn't the proper way, but it worked very quickly:
perframe "markblobs #1.$1; rename #2 centroid id #1.$1.2;" ranges 1,50
[cid:ad953a62-20d2-4851-962a-6645c5c44625]
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.

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.



Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor

Nanoscience & Nanoengineering

South Dakota Mines

501 E. Saint Joseph St., Rapid City, SD 57701

724.510.1253 | Brandon.Scott at sdsmt.edu<mailto:Brandon.Scott at sdsmt.edu>

[South Dakota Mines]<https://www.sdsmt.edu/>

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________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Thursday, October 15, 2020 11:59 AM
To: Scott, Brandon L. <Brandon.Scott at sdsmt.edu>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [EXT] Re: [chimerax-users] Markers from CMM


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Hi Brandon,

  I don't understand your question in enough detail.  Your attached cmm file has lines like:

<marker_set name="track_1">
<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"/>
<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"/>
<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"/>
...
<marker_set name="track_2">
<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"/>
<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"/>
<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"/>
...

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.

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.

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?

Tom



On Oct 14, 2020, at 7:51 PM, Scott, Brandon L. <Brandon.Scott at sdsmt.edu<mailto:Brandon.Scott at sdsmt.edu>> wrote:

Hello all,

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.

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.
perframe "rename #2.$1 track_1 id #1.$2.2;" ranges 1,113 ranges 4,116
perframe "rename #2.$1 track_2 id #1.$2.3;" ranges 114,259 ranges 5,150

Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor
Nanoscience & Nanoengineering
South Dakota Mines
501 E. Saint Joseph St., Rapid City, SD 57701
724.510.1253 | Brandon.Scott at sdsmt.edu<mailto:Brandon.Scott at sdsmt.edu>

[South Dakota Mines]<https://www.sdsmt.edu/>

[South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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