[Chimera-users] Determination of angles formed by distances and ring axes

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 10 17:28:04 PDT 2015


Hi,
The centroid must be a fake atom, or else it would not be possible to draw a distance monitor between it and the other atom.  If you had defined it with Axes/Planes/Centroids, it would not be a fake atom and you couldn’t draw that distance monitor.  So I start out with some confusion.

As far as I understand it, the centroid of some set of atoms should be in the plane based on that same set of atoms.

If I were doing all this with Axes/Planes Centroids (or command “define”), I would:

(1) define a centroid from the atoms of the ring
(2) define a plane from the atoms of the ring
(3) define an axis using just two points, the centroid and the protein atom of interest
(4) define the normal axis from the plane (you have to use Chimera 1.11 daily build and the command for this, e.g. if the plane ID is p1, command: define axis p1)
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-April/010915.html>

… then measure the angle between the two axes, by choosing those two rows in the axes/planes/centroids table of objects, or using their identifiers with the “angle” command.  I just tried all the steps of this process to make sure it works.

Axes/Planes/Centroids:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

“define” command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.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 Jun 10, 2015, at 11:20 AM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I have problems trying to calculate the angle between two lines: one is really built as the distance between a residue atom from a protein and the centroid of a benzene ring (from a ligand), and the other is the line corresponding to the axis of the benzene ring. How could I accomplish this objective? I have read similar issues by chimera-users on the web, but I could not find enough information to complete the calculation (I could only estimate the first distance). In case of problems to clearly comprehend this particular task, please refer to the page 3, Fig 1, panel C in the attached research paper (phi angle).
> 
> PD: Is it normal that the centroid of a benzene ring is above the ring itself? Because in the process of build the first distance, I don't know whether I have to calculate the distance between the centroid and the residue atom (which I found to be shorter), or instead calculate the distance between the center itself of the plane and the residue atom (which would be a bit longer).
> 
> Thanks in advance for your time and assistance in this matter.




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