Hi Fei Li,
The origin is read from the header, but you can change it within Chimera if you want.  Please see these previous posts and further links for more details:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005486.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000961.html>

Best,
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 Sep 4, 2010, at 9:35 AM, Fei Li wrote:

Dear Chimera-dev group,
 
I am a graduate student of Computer Science. I come accross aome problems with the Density map (.mrc file). I noticed that Chimera use the Origin index parameters to locate the density map. I am wondering where these index numbers come from? is it read from the MRC header or does chimera do something about the information in mer header file.
 
thank you for your help.