[chimerax-users] How to define axes in chimeraX

[Elaine Meng]

Hi Bingchun,
ChimeraX is newer and under development, and doesn't (yet) contain some of the features of Chimera.  Some of these are listed in the "Missing Features" section of the ChimeraX download page:
<https://www.rbvi.ucsf.edu/chimerax/download.html>

ChimeraX does not yet have any graphical tool interface to calculating axes, but it does have the "define axes" command and the ability to measure angles and distances of the resulting axes with the "distance" and "angle" commands.
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis>
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>

The "define axis" command was added after the 1.3 release, so you have to download the newer 1.4 daily build to use it.
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

Example commands:
open 2gbp
define axis #1 perHelix true

....then in the Model Panel you can see the axes are under model #1.2, e.g. "helix 1" is #1.2.1, "helix 2" is #1.2.2, etc.  Example command to measure an axis-axis angle:

angle #1.2.1 #1.2.5

You can use any set of atoms to calculate an axis -- i.e. it does not have to be a helix.  See the "define axis" help above for different options of the command.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Feb 10, 2022, at 1:00 PM, Zhao, Bingchun (NIH/VRC) [F] via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
>  
> I’ve been using Chimera to define the axes of my model, then to calculate the angle of approach, by using Tools  Structure analysis  Axes/Planes/Centroids  Define axes
>  
> But I wasn’t able to find out the equivalent function in chimeraX.
> Would you please direct me to that function in ChimeraX?
>  
> Thank you so much!
> Best regards,
> Bingchun
>