Thank you so much for that helpful information! Both the approaches worked! And apologies for the confusion; I realize it now. I meant theta (the green angle) but the angle wrt helical axis (red) is what it looks like when one starts by reading the email’s subject line. But thanks a lot!

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Wednesday, June 28, 2023 at 7:18 PM
To: Das, Abhinaba <abhinaba.das@emory.edu>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: [External] Re: [chimerax-users] Measuring Tilt of Helices

Hi Abhi,
If it is just for measurement (rather than display of the lines per se), you can just use the "Save Info..." button on Axes/Planes/Centroids to write information about the helix axes and then calculate their angles to X,Y,Z axes with trigonometry.
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Faxesplanes.html%23objectlist&data=05%7C01%7Cabhinaba.das%40emory.edu%7C333215daf3ec4fb3465808db782df707%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638235911046440433%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=aew5RGn3fKEMcZgS7SSeljMggJ93mJ0cWzgbtq6W1vI%3D&reserved=0>

If you want some kind of display of these lines in addition to the values, there are probably smarter ways, but how I would do it is to make some dummy atoms that are at two points along each line that you wanted to draw.  Next, calculate axes for each of those dummy-atom pairs using the "define" command or the Axes/Planes/Centroids tool.  Then you can use the usual mechanisms for measuring axis-axis angles ("angle" command or Axes/Planes/Centroids GUI).
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fangle.html&data=05%7C01%7Cabhinaba.das%40emory.edu%7C333215daf3ec4fb3465808db782df707%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638235911046440433%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7HwJVzUs0O3VyCcytC64XEp4GLGSdSqkbIkb92bgSD4%3D&reserved=0>

Actually I don't understand why you want two lines if you just want to measure the tilt of a helix axis relative to the Z axis.  All you need is the line for the Z axis.  Or is it the angle to the XY plane that you want?  I didn't really understand your description.  You could also make some dummy atoms that define the XY plane, and then measure the angle from the helix axis to the plane.

How to make dummy atoms?  If you are reasonably familiar with PDB file format you could just make one (i.e. in your favorite text-editor) containing those atoms, or if you are not, you can use the Build Structure tool (in menu under Tools... Structure Editing), its Start Structure section and the Add "atom" option to add an atom with specific x,y,z coordinates.
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fbuildstructure.html%23start&data=05%7C01%7Cabhinaba.das%40emory.edu%7C333215daf3ec4fb3465808db782df707%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638235911046440433%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9MPsS44Mqr7XwfZqteM1BXexh02TdirL6vmch78ubNE%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 28, 2023, at 2:23 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX users,
> 
> I’m trying to measure the tilt of the helices with respect to the helical axis (i.e. the z-axis). As depicted in the image below, I was wondering if it would be possible to draw a line parallel to the z-axis, traversing through the stack of helices, and another perpendicular to the z-axis and finally measure the angle between the axis passing through the helix (generated by define axis command) and the perpendicular drawn to the z-axis.
> 
> <image001.png>
> 
> Thanks in advance
> Abhi