[chimerax-users] Understanding the output of the align command

[Yazan Abbas]

Hi,

I am trying to make a movie to rotate density in a manner that follows
rotation between two atomic coordinates. To do that, I am aligning the two
models and using the reportMatrix output to inform turn and move commands
in order to transform the density. However, I am encountering some
difficulty, and I'm not sure if this is related to bugs or my lack of
understanding.

For example, if I want to move from the position of model #1 to model #2,
"align #1/b toAtoms #2/b move nothing reportMatrix true" produces the
following:




*Axis 0.11 -0.018 0.99Axis point 166 190 0Rotation angle (degrees) 108Shift
along axis -0.24*

I would think my turn command should be

*turn 0.11,-0.018,0.99 108 models #1 center 166,190,0*

But that doesn't work. I can get it to work if I assume that the reported
axis is x,z,y instead of the expected x,y,z. Also, I have to use a rotation
angle of -108 instead of 108.

I'm not sure if I am using the axis point value correctly though, is it
correct to use that as my center of rotation? It's location (166, 190, 0)
places at the top of the box, which seems unusual to me. And finally, would
I use this same information in a move command (i.e. move axis
distance(shift), as reported by the align command?

Many thanks in advance, I hope explained this clearly.

Best,

Yazan
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