[chimerax-users] Drawing rotation axis in ChimeraX

[lvhailiyaohui]

Hi Elaine and Tom,
    Thanks a lot! I am trying to play around with both of your suggestions. The purpose of our job is to measure the rotated angle for the same model at different states. The following suggestion should be helpful: “There is also a "measure rotation" command that will show an axis of rotation between two models, but that is only if you have moved the two models separately.  It only shows what separate movement you have performed and does not try to calculate anything like an axis of symmetry. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>”. 


I will let you know if I have further questions. Thanks a lot again!


Bests,


Yaohui


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On 03/23/2022 00:12，Elaine Meng<meng at cgl.ucsf.edu> wrote：
Dear Yaohui,
If you mean to display crosshairs at the current center of rotation, try the "cofr" command option with "showPivot", for example:

cofr showPivot true
- or -
cofr showPivot 10,.25

(where the second one specifies a bigger size for the crosshairs).  See "cofr" help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html>

However, if you mean you want to calculate the axis of symmetry of a structure, sorry, there is no command to do that.

There is a "define axis" command but it is for defining the principal component axes of a set of atoms, for example, each helix in an atomic structure:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis>

There is also a "measure rotation" command that will show an axis of rotation between two models, but that is only if you have moved the two models separately.  It only shows what separate movement you have performed and does not try to calculate anything like an axis of symmetry.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>

Finally, there is a "measure symmetry" command to guess the symmetry of a map, but it does not display an axis.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry>

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 22, 2022, at 3:08 AM, lvhailiyaohui via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:

Dear Sir or Madam,
This is Yaohui Li, a ChimeraX user educationally. We are trying to prepare a figure with rotation axis by chimeraX, but haven’g found a way to draw the rotation axis yet. Could you give us any suggestions on drawing the rotation axis in ChimeraX? Thanks a lot! Looking forward to hearing from you!
Bests,
Yaohui
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