The Track Transform module is available as a part of the Segment Volume package. The module is a Chimera extension module. You will need the Chimera software package to use this module.
The module helps track 3D transformation (3D translation and 3D rotation) of a model displayed in Chimera (in terms of the camera coordinates). It can record a starting orientation and position of a model, and then set the orientation and position of another or the same model to that of the recorded transformation.
Note: This version of the Segment Volume package is a pre-release version.
The module files are stored in the directory SegmentTrack. To list the module under Chimera's Tools menu, add the directory - containing - the SegmentTrack directory to Chimera's list of Tools.
To do so, open Chimera's main window, choose Perferences under Favorites menu, then choose the Tools category and then Add the directory - containing - the SegmentTrack directory. This will list the tool under AIRS on the Tools menu.
To start the module from the Chimera menu, first you will need to ensure that the module is listed under Chimera's Tools menu. Then, click on Track Transform in the AIRS menu, under Chimera's Tools menu.
Alternatively, you can use the command line tool in Chimera's IDLE tool (under Programming tools on the Tools menu), and type:
>>> import SegmentTrack
>>> SegmentTrack.trackxform.show_track_xform_dialog()
The Model menu lists all Chimera open models and keeps track of any newly opened or closed models.
To use the module, you will first need to select an open model from Model menu and record its current orientation by pressing the Record button. The translation axes and the rotation axes and angle parameters are recorded and displayed.
To get the current transformation of a model, select that model from the Model menu and press the Get button.
To apply the recorded transform, select the models in Model List to which you want to apply the recorded transform and press the Apply button. Each of the selected models' orientation and center are individually set to the recorded transformation parameters.
The Reset button simply resets all the transform parameters to 0.
The Close button closes the dialog, and the Help button launches this help page.
In the first figure, we have one model which is broken up into three small models. We record the transform of the parent model by selecting the parent model on the Model menu, and hitting the Record button. Then, we pick the child and the parent models and move them around in Chimera. The final states are shown in the second figure. Now, when we select all the four models in the Model List box, and hit the Apply button, then all the models return to the recorded transform position as shown in the first figure.
To get the transform object of a Chimera model, simply type:
>>> import SegmentTrack
>>> SegmentTrack.trackxform.get_xform(model)
To get help, type:
>>> help(TrackXform.get_xform)
To apply the transform object to a Chimera model, simply type:
>>> import SegmentTrack
>>> SegmentTrack.trackxform.update_xform(model, xform)
To get help, type:
>>> help(SegmentTrack.trackxform.update_xform)
Even if a model is not active (see Chimera's Model Panel), its orientation and center are set to the recorded transformation.