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

Hi Dave, The reason the spheres look solid is that "surface capping" is turned on by default. You can just turn off surface capping so that they will look like thin shells when clipped. There are a bunch of ways to show the capping dialog, but one easy way is to click "Cap clipped surfaces" on the Side View. In the dialog, just uncheck "Cap surfaces at clip planes". I don't think we have any command to do that, or any preference for capping to be turned off, sorry. Formerly capping was off by default, which is why the button says "Cap clipped surfaces" instead of "Uncap" or "Control surface capping" which would be more descriptive of the current situation. The things created with the "shape" command are surface models, and you can select them, show them as mesh, change their colors, make them transparent, etc. using the Actions... Surface menu or the Selection Inspector. 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 On Mar 10, 2009, at 1:58 PM, David Chenoweth wrote:

Hi Elaine,

I need to do something very similar to the procedure that you sent to Bala for placing a sphere at a designated location except I need to place shells of concentric spheres at a point in space. I can use the command below to place multiple spheres at a point but the spheres are filled with the color. I would like to have just a thin shell or the surface of multiple spheres placed at a point that increment in their radius by 1 angstrom intervals. I would then like to make the spheres slightly transparent so I can overlay them on top of the resolution dependent fourier ripples for a heavy atoms electron density map. Any ideas?

Thanks, Dave Chenoweth