[Chimera-users] report rotate and shift value in MatchMaker

[Yanhe Zhao]

Dear Elaine,

Thank you so much. I will read and see whether I can figure it out.

Thanks and have great ones,
Yanhe

Elaine Meng <meng at cgl.ucsf.edu> 于2022年1月5日周三 15:44写道：

> Hi Yanhe,
> This is not my area of expertise, but I believe it is a standard
> mathematical representation of 3D rotation and translation.  There are lots
> of explanations on the web, e.g. like  the "Tr" translation-rotation matrix
> in this page, with the bottom row omitted as discussed therein:
>
> <http://fastgraph.com/makegames/3drotation/>
>
> All I know personally is what is already written in the help for "measure
> rotation":
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jan 5, 2022, at 10:30 AM, Yanhe Zhao via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Elaine,
> > Sorry, maybe it's stupid question, but take your example here:
> >
> > rotation x ?         rotation y ?       rotation z?    shift ?
> > -0.33209740  -0.83501915  -0.43869618  55.73384197  Row1
> >  -0.20519447   0.51790962  -0.83046063  20.74214411 Row2
> >  0.92065550  -0.18577579  -0.34333775 -49.60904344  Row3?
> >
> > Why there are three rows? If I was wrong please forgive me.
> >
> > Thanks and cheers,
> > Yanhe
> >
> > Elaine Meng <meng at cgl.ucsf.edu> 于2022年1月5日周三 12:10写道：
> > Hi Yanhe,
> > The matrix just includes the total shift and total rotation of one model
> relative to another... there is nothing like iteration.   What the matrix
> means is explained in the "measure rotation" help:
> > <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation
> >
> >
> > In the Log, the shift is also given in a second way, as an axis (which
> can be pointed in any direction) and the total shift along that axis.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > > On Jan 5, 2022, at 9:58 AM, Yanhe Zhao via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > >
> > > Dear Elaine,
> > >
> > > It's my fault: the fourth column is the shift value after rotation,
> and the value along axis (for example the axis is z) was reported. What is
> shift value in another two dimensions? And the three row means three
> iteration?
> > >
> > > Thanks and cheers,
> > > Yanhe
> > >
> > > Elaine Meng <meng at cgl.ucsf.edu> 于2022年1月5日周三 11:46写道：
> > > Hi Yanhe,
> > > At least for me, it does give both the shift and rotation.  The shift
> is the last part. For example, I used matchmaker to superimpose 2gbp and
> 2fw0 and then "measure rotation" gives this in the Log:
> > >
> > > Position of 2gbp (#0) relative to 2fw0 (#1) coordinates:
> > >   Matrix rotation and translation
> > >     -0.33209740  -0.83501915  -0.43869618  55.73384197
> > >     -0.20519447   0.51790962  -0.83046063  20.74214411
> > >      0.92065550  -0.18577579  -0.34333775 -49.60904344
> > >   Axis   0.39527163  -0.83345089   0.38616052
> > >   Axis point  46.43348863   0.00000000  -0.96285927
> > >   Rotation angle (degrees) 125.36356888
> > >   Shift along axis -14.41460560
> > >
> > > Best,
> > > Elaine
> > > -----
> > > Elaine C. Meng, Ph.D.
> > > UCSF Chimera(X) team
> > > Department of Pharmaceutical Chemistry
> > > University of California, San Francisco
> > >
> > >
> > > > On Jan 5, 2022, at 9:36 AM, Yanhe Zhao via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > > >
> > > > Dear Elaine,
> > > >
> > > > Thanks a lot. It is so helpful. I try command ' measure rotation #17
> #13', the rotation value was reported, but no shift value, should I add
> more option?
> > > >
> > > > Thanks and cheers,
> > > > Yanhe
> > > >
> > > > Elaine Meng <meng at cgl.ucsf.edu> 于2022年1月5日周三 11:20写道：
> > > > Hi Yanhe,
> > > > Happy New Year!
> > > >
> > > > To get the rotate/shift of one model compared to another after they
> have been moved separately (such as by using Matchmaker), you can use the
> Chimera "measure rotation" command.
> > > >
> > > > See <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation
> >
> > > >
> > > > ChimeraX also has both of these features, Matchmaker and the
> "measure rotation" command, although the details of how to use them are
> slightly different.
> > > >
> > > > I hope this helps,
> > > > Elaine
> > > > -----
> > > > Elaine C. Meng, Ph.D.
> > > > UCSF Chimera(X) team
> > > > Department of Pharmaceutical Chemistry
> > > > University of California, San Francisco
> > > >
> > > >
> > > > > On Jan 5, 2022, at 8:04 AM, Yanhe Zhao via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > > > >
> > > > > Greeting there,
> > > > >
> > > > > Happy New Year!
> > > > >
> > > > > How can find the rotate and shift value after I done the
> 'MatchMaker' in Chimera?
> > > > >
> > > > > Thanks and regards,
> > > > > Yanhe
>
>
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