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

[Yazan Abbas]

Hi Elaine,

What I am actually doing is making a movie showing a morph between
different atomic coordinates. There is unmodelled density that I wish to
move/rotate along the same trajectory that one of the chains is moving. I
found that using the turn or roll command to move the density alongside the
coordset command which shows the model morph works well enough. However,
turn or roll around the y axis is not as precise as an axis of rotation
that is determined by the align command, which is what I am trying
to achieve.

Best,

Yazan

On Tue, Aug 13, 2019 at 6:51 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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