CCL: suggestions for manual docking and building
- From: Elaine Meng <meng]*[cgl.ucsf.edu>
- Subject: CCL: suggestions for manual docking and building
- Date: Mon, 30 Jan 2006 10:22:43 -0800
Sent to CCL by: Elaine Meng [meng:-:cgl.ucsf.edu]
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|*|umich.edu wrote:
Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
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
- Free. Or cheap. Or at least a good value worthy of an investment.
I welcome all suggestions, and will summarize what I learn.
Department of Biological Chemistry
University of Michigan Medical School
Ann Arbor, MI 48109-0606
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