CCL: suggestions for manual docking and building

 Sent to CCL by: Elaine Meng []
 Chimera might fill the bill, see
 - reads in PDB and Mol2 formats, among others
 - each structure can be toggled between fixed and movable
 with the mouse, using checkboxes below the command line
 or in the Model Panel
 - free for noncommercial use and available for Windows,
 Mac (requires X11), Linux, etc.; easy download/install
 - includes documentation and tutorials that can be
 accessed from its Help menu
 On Jan 29, 2006, at 1:49 PM, Bruce Palfey brupalf|*| wrote:
 Sent to CCL by: Bruce Palfey [brupalf^-^]
 I was wondering if people could suggest a good program for manually
 and interactively building protein-ligand or nucleic acid-ligand
 complexes.  Characteristics of the ideal program are:
 - Direct.  I'd like to be able to grab one molecule and maneuver it
 into a position I think is interesting using simple, direct mouse and/
 or keyboard controls.
 - Easily loaded.  The molecules - either macro or micro - would most
 likely come from different pdb files, though support of other formats
 would also be helpful.  A minimum of file preparation/conversion is
 - Intuitive.  The students who pass through my lab should be able to
 just pick it up and go; we need a tool to support our research,
 rather than a system to dedicate our efforts to mastering.
 - Available for common cheap platforms.  I'd like to use this on PC's
 in my lab or on my Mac laptop, or both.
 - Supports hardware stereo.  It seems to me that that's the best way
 to build.
 - Free.  Or cheap.  Or at least a good value worthy of an investment.
 I welcome all suggestions, and will summarize what I learn.
 Bruce Palfey
 Department of Biological Chemistry
 University of Michigan Medical School
 Ann Arbor, MI 48109-0606
 Elaine C. Meng, Ph.D.                          meng,
 UCSF Computer Graphics Lab and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco