[Chimera-users] report rotate and shift value in MatchMaker
Yanhe Zhao
yanhezhao1990 at gmail.com
Thu Jan 6 06:42:25 PST 2022
Dear Tom,
Thanks you so much.
Yes, I will follow your way to measure the shift value of my case.
Thanks and have great day,
Yanhe
On Wed, Jan 5, 2022, 5:54 PM Tom Goddard <goddard at sonic.net> wrote:
> 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> 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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