[Chimera-users] Angle

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 24 09:39:50 PDT 2014

Hi Jian,
Oh, I thought you were using “axes” as created with the command “define” or the tool “Axes/Planes/Centroids.”  Those axes are meant to work with various angle and distance measurements.

The things that you get from “measure rotation” are totally different.  They are not Chimera axes but marker models made of 2 “markers” (fake atoms) with a bond between them.  In that case, you would follow the instructions for using the “angle” command with atoms.  If you are using all 4 atoms (both ends of each marker model from “measure rotation”), you are measuring a dihedral angle.  It is unclear what order the 4 atoms are being taken in if you just specify #1 #2.  To know exactly what measurement you are getting, you should pick the 4 atoms in the desired order (shift-ctrl-click) and then use “angle sel”.  If you use the option “dihedral false” it will give the angle between the 1-2 and 3-4 vectors instead of the 1-2-3-4 dihedral angle.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 24, 2014, at 9:22 AM, Jian Guan <jug25 at psu.edu> wrote:

> Hi Elaine,
> Thank you so much for your reply. I made the axes by myself through “measure rotation”. It generated axes models. If “angle” command only show the smaller angle, why I got angle of minus and even more then 90 degree?
> Thanks,
> Jian
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: 2014年9月23日 16:36
> To: Jian Guan
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Angle
> Hi Jian,
> You would need to use the IDs of the axes (not model numbers) in the angle command.  The IDs are shown in the Axes/Planes/Centroids list of objects. You could have specified the IDs when you made the axes, or they would be generated automatically.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> So the command would be something like:
> angle a1 a2
> It gives the smaller angle, treating both axes as infinite lines.
> Elaine
> On Sep 23, 2014, at 12:29 PM, "Jian Guan" <jug25 at psu.edu> wrote:
> > Hi All,
> > I made two axes for two molecule, and want to measure the angle between them. Let's say, #1 and #2 are the two axes. I used command line of "angle #1 #2" to do that.
> > Question:
> > What is the default angle measurement? The #1 rotate clockwise or anti-clockwise to reach #2?
> > Thanks,
> > Jian
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