Hi Jian,
There is no "dock prep" command, but there are commands "addh" and "addcharge":
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>

Some other parts of Dock Prep can also be done with commands (for example "delete solvent"), but python scripting may be required for certain steps if you need them.  I cannot advise on the python part, perhaps others can.

For scripting to handle multiple structures, please see previous posts such as:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html>

I hope this helps,
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 Oct 20, 2009, at 5:51 PM, Bisn wrote:

Hello,

We are Chimera users trying to process 1000 proteins, e.g., add

hydrogen and charge. We want to do this via a Chimera for DOCK

preparation.

I know that Chimera accepts command line, but this is not realizable

for processing 10000 molecules. Have you any idea of the task?

Thanks!

Jian Chen