Dear Reiner, Chimera does not do any automated docking. Instead, it provides a tool (ViewDock) for viewing your results from the separate program DOCK. For information about DOCK, see http://dock.compbio.ucsf.edu/ The DOCK people also have mailing lists for questions and discussion about their program, see http://dock.compbio.ucsf.edu/contact_info/index.htm More generally, different docking programs handle the problem differently, so it will depend on what you decide to use. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 20, 2005, at 5:44 AM, Reiner Villavicencio wrote:
Dear all, I have read a couple of literature which uses the Chimera program. Before performing a docking run, most of them selects only the relevant residues within a certain region (for example in a 20 angstrom core). May I ask how is this done in Chimera? I mean do the "unrelevant" portions get deleted? Thank you and good day - RV
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