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