<div dir="ltr">Dear Elaine,<div><br></div><div>Thank you so much. I will read and see whether I can figure it out.</div><div><br></div><div>Thanks and have great ones,</div><div>Yanhe</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> 于2022年1月5日周三 15:44写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Yanhe,<br>
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:<br>
<br>
<<a href="http://fastgraph.com/makegames/3drotation/" rel="noreferrer" target="_blank">http://fastgraph.com/makegames/3drotation/</a>><br>
<br>
All I know personally is what is already written in the help for "measure rotation":<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jan 5, 2022, at 10:30 AM, Yanhe Zhao via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi Elaine,<br>
> Sorry, maybe it's stupid question, but take your example here:<br>
> <br>
> rotation x ? rotation y ? rotation z? shift ?<br>
> -0.33209740 -0.83501915 -0.43869618 55.73384197 Row1<br>
> -0.20519447 0.51790962 -0.83046063 20.74214411 Row2<br>
> 0.92065550 -0.18577579 -0.34333775 -49.60904344 Row3?<br>
> <br>
> Why there are three rows? If I was wrong please forgive me.<br>
> <br>
> Thanks and cheers,<br>
> Yanhe<br>
> <br>
> Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> 于2022年1月5日周三 12:10写道：<br>
> Hi Yanhe,<br>
> 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:<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation</a>><br>
> <br>
> 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. <br>
> <br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D. <br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> <br>
> > On Jan 5, 2022, at 9:58 AM, Yanhe Zhao via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> > <br>
> > Dear Elaine,<br>
> > <br>
> > 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?<br>
> > <br>
> > Thanks and cheers,<br>
> > Yanhe<br>
> > <br>
> > Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> 于2022年1月5日周三 11:46写道：<br>
> > Hi Yanhe,<br>
> > 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:<br>
> > <br>
> > Position of 2gbp (#0) relative to 2fw0 (#1) coordinates:<br>
> > Matrix rotation and translation<br>
> > -0.33209740 -0.83501915 -0.43869618 55.73384197<br>
> > -0.20519447 0.51790962 -0.83046063 20.74214411<br>
> > 0.92065550 -0.18577579 -0.34333775 -49.60904344<br>
> > Axis 0.39527163 -0.83345089 0.38616052<br>
> > Axis point 46.43348863 0.00000000 -0.96285927<br>
> > Rotation angle (degrees) 125.36356888<br>
> > Shift along axis -14.41460560<br>
> > <br>
> > Best,<br>
> > Elaine<br>
> > -----<br>
> > Elaine C. Meng, Ph.D. <br>
> > UCSF Chimera(X) team<br>
> > Department of Pharmaceutical Chemistry<br>
> > University of California, San Francisco<br>
> > <br>
> > <br>
> > > On Jan 5, 2022, at 9:36 AM, Yanhe Zhao via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> > > <br>
> > > Dear Elaine,<br>
> > > <br>
> > > 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? <br>
> > > <br>
> > > Thanks and cheers,<br>
> > > Yanhe<br>
> > > <br>
> > > Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> 于2022年1月5日周三 11:20写道：<br>
> > > Hi Yanhe,<br>
> > > Happy New Year!<br>
> > > <br>
> > > 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.<br>
> > > <br>
> > > See <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation</a>><br>
> > > <br>
> > > ChimeraX also has both of these features, Matchmaker and the "measure rotation" command, although the details of how to use them are slightly different.<br>
> > > <br>
> > > I hope this helps,<br>
> > > Elaine<br>
> > > -----<br>
> > > Elaine C. Meng, Ph.D. <br>
> > > UCSF Chimera(X) team<br>
> > > Department of Pharmaceutical Chemistry<br>
> > > University of California, San Francisco<br>
> > > <br>
> > > <br>
> > > > On Jan 5, 2022, at 8:04 AM, Yanhe Zhao via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> > > > <br>
> > > > Greeting there,<br>
> > > > <br>
> > > > Happy New Year! <br>
> > > > <br>
> > > > How can find the rotate and shift value after I done the 'MatchMaker' in Chimera?<br>
> > > > <br>
> > > > Thanks and regards,<br>
> > > > Yanhe<br>
<br>
</blockquote></div>