[chimerax-users] Markers from CMM

[Tom Goddard]

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> 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>
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