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

[Elaine Meng]

Hi Yazan,
I’d recommend instead using fitting (e.g. “fitmap” command or “Fit in Map” tool) to make the map align to the atomic model(s) as needed once you’ve moved them to different positions, or if the map and atoms are already aligned, just always move them together rather than separately.  I.e. if you’re rotating, why not move both the atomic and map models in the same rotation command (“turn” or “roll”)??

You can save each set of model positions with command “view name” and then later (in the movie script) use “view” to reset to the previously saved positions over multiple frames.  The positions are saved in sessions so you can set it all up ahead of time before running the script of the movie part.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name>

Personally I wouldn’t even try to deal with matrices.  It is much too confusing (at least to me) and depends on the map and atom coordinates already being fit to each other before you open them.  Note, however, there is also a “view matrix” command to apply a tranformation matrix, which might make it slightly less confusing than trying to apply it with other commands.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> 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