[Chimera-users] center of the molecule

David Chenoweth dchen at caltech.edu
Tue Mar 10 13:58:53 PDT 2009

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  

Dave Chenoweth

On Mar 10, 2009, at 10:46 AM, Elaine Meng wrote:

> 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 at 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.
> <centroid.f>
> 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
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