Save position matrices for subtomogram boxes

[m-schmid@…]

Would like to be able to write out the position matrices for subtomogram boxes. This is useful after using volume resample to create tens of subvolumes in VR by moving around a template volume. Then those volumes are saved

save boxes%03d.mrc models #4-35

Would like to save the matrices too perhaps with

save boxes%03d.mrc models #4-35 matrices boxes.positions

and also just the matrices could be saved

save boxes.positions models #4-35

The written boxes.positions could have one line per model giving the model name followed by 12 numbers giving the 3x4 positioning matrix.

It would also be useful to read in these matrices and place copies of a new map (subtomogram average) at each of those positions.

[Tom Goddard]

Added "positions" file format.

The positions file gives positions of any type of model (not just volumes) and has one line per model giving the model name and 12 numbers which are the position 3x4 matrix separated by commas. You can save this file with

save boxes.positions models #4-35

I did not add the ability to save them at the same time as saving MRC files. You can also open the positions file applying the matrices to specified models as in

open boxes.positions models #10-41

That ignores the names of the models and simply assigns the matrices in order. If you want it to match the model names then use the matchNames option

open boxes.positions models #10-41 matchNames true

By default open and save of positions does not c onsider child models. So if volume are specified it won't save the surface submodels of the volume. That is good because the surface submodel is generally not moved relative to its parent volume model. But if you want to save child models or set positions of child models use the open/save option "childModels true".

This positions file is like the file written by Chimera classic matrixget command and read by the matrixset command. But that file does not list model names, instead it included model id numbers. Also it put the id on one line and 3x4 matrix on 3 lines.