[Chimera-users] need a script

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 26 09:48:22 PST 2009

Hi Bala,
The "distance" command measures distances and (by default) shows  
dashed lines and the distance values in the main window.  The distance  
at the time of command execution is also reported in the Reply Log.   

dist #0:35 at ca #1:35 at ca

You can control the appearance of those distance monitors, for example  
to hide the distance values:

setattr p label " "

To show arrows, however, the only way I know aside from python coding  
is to create a BILD format file describing the arrows and read it in.   
The format is pretty simple.  For example, reading in a file  
arrow.bild containing this line:

.arrow 17.675  49.049  21.434 16.956  48.582  17.728

makes an arrow between the two sets of xyz coordinates.  You can also  
control its thickness, color, etc. and make other shapes, and of  
course put many of them in one file.  See the BILD description:


Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 26, 2009, at 3:20 AM, Bala subramanian wrote:

> Dear Chimerians,
> Kindly help me If anybody has a script to do the following.
> Given two pdb files, the script should calculate the vector distance  
> between the atoms, say CA atoms and draw an arrow representing the  
> magnitude and direction of the vector. Do i need to add some plugin  
> to draw arrows through atoms in Chimera.
> Thanks in advance,
> Bala

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