[Chimera-users] report rotate and shift value in MatchMaker
Tom Goddard
goddard at sonic.net
Wed Jan 5 15:54:06 PST 2022
Hi Yanhe,
Here is some more explanation of the measure rotation output. The 3 row by 4 column matrix gives the rotation and translation. The first column is the x-axis unit vector of 2gbp in 2fw0 coordinates. The second column is the y-axis unit vector and the third column is the z-axis unit vector. The fourth column is a translation again in the 2fw0 coordinate system. First the rotation is applied then the translation (the order matters). This form of the rigid motion is used by some software and file formats like the PDB file BIOMT remark records.
Below the matrix is another equivalent description of the same rotation given by a rotation axis, a point on that axis, a rotation angle and a shift along the axis. Those 4 parameters (axis and point in 2fw0 coordinate system) describe the same position as the matrix but may be more useful -- you may only be interested in the rotation angle for instance, 125 degrees in this example. With this set of parameters there is no shift perpendicular to the axis.
You asked about translation. In a rigid motion there is no one translation vector -- the translation depends on where the center of rotation is taken. Maybe you want the translation of the center of the moved model. The output here does not directly tell you that. For that you might open two copies of the model you want to move, just move one of them, then measure the distance between the two copies using the Chimera distance between atoms -- just measure the distance between two equivalent atoms in the moved and unmoved structures.
Tom
> 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
> 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 <mailto: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 <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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <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 <mailto: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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