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

[Tom Goddard]

Hi Yazan,

  Each model has its own coordinate system, and there is the global coordinate system of the scene.  If you haven't moved any of the models (by aligning, match maker, fitting, move selected mouse mode, move command with models option, ...) then all those coordinates match up.  If you have moved some models and then you want to apply a rotation you have to know 1) what coordinate system you got the rotation axis and angle for, and 2) what coordinate system you are using when you apply the rotation.  For 1) you are using the align command to get the rotation.  You didn't include the relevant output from the align command in your post where it says the matrix is in the coordinate system of the first model in the align command.  You then try to apply that with the turn command and since you didn't specify a coordinate system it is using the scene coordinates.  Obviously that is not going to work if the first model in the align command was already moved and has a different coordinate system than the scene coordinates.  You could specify the coordinate system in the turn command (option "coordinateSystem #1") which says what coordinate system the rotation axis and center point are in.

  But I'm with Elaine, you are trying to do something too tricky, and you are going to have to know exactly what you are doing, including the above multiple coordinate system details to get it to work.

  You might find the "view position #3 sameAs #1" command to be useful -- it moves model #3 to have the same coordinate system as model #1.  So if #3 is something you want to move along with model #1 you can keep executing that command to make them track each other.  There are other tricks, like you could make model #3 a submodel of #1 so it automatically is dragged along with model #1.

	Tom


> On Aug 13, 2019, at 3:34 PM, Yazan Abbas <yazan.abbas at gmail.com> wrote:
> 
> 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 0.99
> Axis point 166 190 0
> Rotation angle (degrees) 108
> Shift 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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