HI Elaine, Wow, get it. You make my brain clear. Now I know what the angle is. Thank you so much. Sincerely yours, Jian -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: 2014年9月24日 12:40 To: Jian Guan Cc: chimera-users BB Subject: Re: [Chimera-users] Angle 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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> I hope this helps, Elaine ----- 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@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@cgl.ucsf.edu] Sent: 2014年9月23日 16:36 To: Jian Guan Cc: chimera-users@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/structureme as/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@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users