Hi Bala, I'm sure this is done several places in the code, but we don't currently have user interface centroid calculation (although this is planned for the future). However, I thought of a little trick to get the information from Chimera: (a) select the atoms you want to include in the calculation (b) command: reset (c) command: focus sel Then the center of rotation, reported in the status line and Reply Log, will be the geometric (non-mass-weighted) centroid of that set of atoms. It is very important to reset so that the coordinates are not transformed from the input file, and then without moving the structure yourself, use focus. If you move the molecule yourself between reset and focusing on the selected atoms, the result will be incorrect. You can test the result by making a little sphere at that position (requires recent build, version 1.4) with the shape command and seeing if it looks reasonable. For example, open 2gbp select ligand reset focus sel shape sphere center 37.25,30.64,49.52 coord #0 radius 0.4 color red I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. for those who don't mind using fortran programs, I attach a little one I wrote a long time ago that prompts the user for an input PDB file and then calculates the non-mass-weighted centroid and radius of gyration using all the atoms in the file. Caveat emptor. On Mar 10, 2009, at 7:08 AM, Bala subramanian wrote:
Dear Friends,
How can i get the x,y,z of the center of the loaded molecule in chimera. While i do box generation generation for DOCK program, i want to tell the script to construct box by considering the x,y,z center of the molecule.
Thanks, Bala