[chimerax-users] A question about model position matrix

[Zheng Ruan]

Dear ChimeraX users,

I'm trying to understand the model position matrix. According to the
documentation, "Each matrix is reported as 12 comma-separated numbers,
corresponding to a 3x3 rotation matrix and a translation vector in the
fourth column. Ordering is row-by-row, such that the translation vector is
given as the fourth, eighth, and twelfth numbers."

When I load a model into ChimeraX and use "view matrix" command to check
the model position, I got
"#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0". The rotation
matrix for #1 is an identity matrix with translation vector to be 0 for all
directions.

However, if I rotate the model using the command "turn z 90 models #1" and
then check the model position using "view matrix", I got something like
"#1,1.1102e-16,-1,0,689.33,1,1.1102e-16,0,-1.9358,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0".
The translation vector for #1 becomes (689.33, -1.9358, 0).

Since I only applied a simple rotation of the model along z-axis, why the
translation vector becomes non-zero in this case? I hope to have a better
understanding of how ChimeraX handles the model position matrix to describe
model positions.

Thank you so much!
Best,
Zheng
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