[Chimera-users] Rendering a vector/axis

Richard Stanton rstanton1 at student.gsu.edu
Tue Feb 23 10:36:55 PST 2010

Thanks Elaine, but I still cannot get the axis to display.  Would it matter that I have defined it using multiple models?  I have attached a screen shot with the structure measurement window open and my "axis_GDP" plane defined and the "shown" box checked but there is no cylinder.  I have made a polymeric structure of many separate protein models and am tying to link them using vectors.


From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Tuesday, February 23, 2010 1:18 PM
To: Richard Stanton
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Rendering a vector/axis

Hi Rich,
That is the whole purpose of the tool, to view axes and other derived
objects and perform measurements between them.  The axis or axes
should be displayed as cylinders and listed in the Structure
Measurements dialog as soon as you define them.  Perhaps you are doing
something wrong?

Here is the documentation for Axes/Planes in Chimera 1.4:

and in Chimera 1.5 (daily builds), it has been expanded to Axes/Planes/

The dialog listing the axes includes color wells for changing their
colors and allows choosing two axes and getting distances/angles.  If
you get Chimera version 1.5, you can also make the measurements
involving axes with the "distance" and "angle" commands.

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 Feb 23, 2010, at 9:51 AM, Richard Stanton wrote:

>  Hi,
> Is there a way to render a vector after defining it as an axis in
> the "Axes/Planes" tab under "Structure Measurements"?  I am able to
> define an axis using the selected atoms in my structure but I am not
> sure how to visually render and alter its appearance, as there is no
> visual representation on the graphics screen.  I was hoping that
> after using my selected atoms to define the axis I would then have
> an arrow or line showing me the axis/vector and I could then create
> different vectors/axis and view them simultaneously to show the
> difference between their angles.  Is there a way to do this?
> Thanks in advance for the help!
> Thanks,
> Rich

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