[Chimera-users] Specifier for the z-axis

[Yang Shi]

Dear Elaine,

This is a brilliant idea. Many thanks!

Best wishes,
Yang

> On 30 Jan 2023, at 06:33, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Yang,
> Sorry, there is no option to specify a model's X, Y, or Z axis in the "angle" command. Other than doing the  math yourself with the axis information (e.g. use Save on the Axes/Planes/Centroids dialog to write info to a file), the only idea I have is to:
> 
> (1) use Build Structure, the Start Structure option to add 2 atoms that are along the Z axis, e.g. with x y z coordinates:
> 0 0 0
> 0 0 100
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
> 
> Make sure that these two atoms are not moved separately from the map, so that they will be in the same coordinate system of the map.
> 
> (2) define axis for those two atoms
> 
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html>
> 
> (3) then measure angle between the axis created as described above and the plane
> 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
> 
> 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 28, 2023, at 5:20 AM, Yang Shi via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear Chimera-Team,
>> 
>> I am wondering if there is a specifier for the z-axis of a map. I would like to measure the angles between defined plains and Z-axis.
>> 
>> Best wishes,
>> Yang