[chimerax-users] A question about model position matrix

[Zheng Ruan]

Hi Elaine,

Thank you for the reply. However, I don't see a large translation of my map
after I type the "turn" command. I only have one map loaded in ChimeraX and
the map is rotated about its own z-axis.

I also tried to specify the "center" option as suggested, but I still see a
large translation value. For example,

*open volume.mrc **format mrc*

*view matrix*
camera position: 1,0,0,345.63,0,1,0,343.7,0,0,1,1042.6
model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0

*turn z 90 models #1 center #1*

*view matrix*
camera position: 1,0,0,345.63,0,1,0,343.7,0,0,1,1042.6
model positions: #1,1.1102e-16,-1,0,689.33,1,1.1102e-16,0,-1.9358
,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0

I also tried to change the center of rotation, but the result remains the
same.

Best,
Zheng


On Thu, Mar 31, 2022 at 11:20 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Zheng,
> I believe it is because the center of rotation from your command is not
> the same as the center of the model.  If the center of rotation is far from
> the model, it might be translated a large distance in addition to being
> rotated.  You can specify the center of rotation for the "turn" command
> with the "center" option.  I believe that if you use
>
> turn z 90 models #1 center #1
>
> ...the translation of the model would then be zero or close to zero.
>
> See help for "turn"
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Mar 30, 2022, at 8:18 PM, Zheng Ruan via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Dear ChimeraX users,
> >
> > I'm trying to understand the model position matrix. According to the
> documentation, "Each matrix is reported as 12 comma-separated numbers,
> corresponding to a 3x3 rotation matrix and a translation vector in the
> fourth column. Ordering is row-by-row, such that the translation vector is
> given as the fourth, eighth, and twelfth numbers."
> >
> > When I load a model into ChimeraX and use "view matrix" command to check
> the model position, I got
> "#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0". The rotation
> matrix for #1 is an identity matrix with translation vector to be 0 for all
> directions.
> >
> > However, if I rotate the model using the command "turn z 90 models #1"
> and then check the model position using "view matrix", I got something like
> "#1,1.1102e-16,-1,0,689.33,1,1.1102e-16,0,-1.9358,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0".
> The translation vector for #1 becomes (689.33, -1.9358, 0).
> >
> > Since I only applied a simple rotation of the model along z-axis, why
> the translation vector becomes non-zero in this case? I hope to have a
> better understanding of how ChimeraX handles the model position matrix to
> describe model positions.
> >
> > Thank you so much!
> > Best,
> > Zheng
>
>
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