[Chimera-users] Distance between helices

[Elaine Meng]

Hi Andy,
You can measure atom-atom distances, or you can measure the distance  
between the helix axes.

There are several ways to measure atom-atom distances, including Ctrl- 
click to select the first atom, Shift-Ctrl-click to select the second  
atom, and then clicking "Create" in the "Distances" tool (under  
Tools... Structure Analysis):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances

You would have to display the atoms to pick them from the screen, but  
you could undisplay them after that.  Or instead of picking from the  
screen, you could name them in a distance command, for example:
distance :10.a at ca :10.b at ca
In that case the atoms never need to be displayed; to see the distance  
you would need to look at the "Distances" tool.

If instead you want to use the helix axes for the measurements, use  
the "Axes" tool (under Tools... Structure Analysis):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes

Using that tool, define the helix axes, and then in the resulting list  
choose the two of interest with the mouse.  That will show the axis- 
axis distance and crossing angle on the dialog and in the Reply Log.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Jul 28, 2008, at 10:35 AM, Thomas Goddard wrote:

> HI Tom
>  How do I compute and   show the distance between 2 regions (2 alpha
> helixes)  of  2 crystal structures (docked in the density maps),  
> similar
> portions of each is already highlighted/selected to show the DNA  
> binding
> region (without showing the atoms).
>
> THanks
> Andy
>
> Dr. Anindito Sen (Ph.D)
> Research Associate , Dept. of Biochemistry and Molecular Genetics
> University
> of Virginia
> Box 800733 Charlottesville, VA 22908