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

[Yazan Abbas]

Thanks Tom,

You are right, I did miss the part of the output where it tells me which
coordinate system it is using.

Cheers,

Yazan

On Tue, Aug 13, 2019 at 7:44 PM Tom Goddard <goddard at sonic.net> wrote:

> 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 0.99Axis 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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