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. Example: dist #0:35@ca #1:35@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: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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