[Chimera-users] drawing spheres with various radii

Roni Rayes rfr06 at fsu.edu
Wed Nov 3 11:24:48 PDT 2010

Hi Elaine,

I was able to draw the sphere using shape sphere. Now having troubles with changing radii of sphere (to specific length in Angstrom) and changing center of sphere (to a specific atom). Could you advise me on that.

Sorry for bothering you again,

Thanks for your time,


----- Original Message -----
From: Elaine Meng <meng at cgl.ucsf.edu>
Date: Wednesday, November 3, 2010 1:04 pm
Subject: Re: [Chimera-users] drawing spheres with various radii
To: Roni Rayes <rfr06 at fsu.edu>
Cc: chimera-users at cgl.ucsf.edu

> Hi Roni,
> I don't know what you mean by "from one atom."  There are several 
> ways to draw spheres.  
> You can use the "shape sphere" command to simply draw a spherical 
> surface of specified size, color and location.  You could center it 
> on an atom.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere>
> You can create a BILD format file with a sphere in it (that would 
> be one line) and read it in.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
> You can use the "molmap" command to simulate density maps from 
> atoms, or your one atom.  Then in Volume Viewer you could adjust 
> the isosurface contour level on that density map.  I haven't tried 
> this on only one atom, not sure how good it would look.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> Or, you can place a marker (which is a fake atom and can be shown 
> as ball or sphere) using Volume Tracer.
> Or, you could make a PDB file with the fake atoms in it and read it 
> in.
> I hope this helps
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Nov 3, 2010, at 9:48 AM, Roni Rayes wrote:
> > Hello,
> > We are trying to model the FRET data we obtain by drawing spheres 
> from one atom.
> > I know VMD does that, however we are trying to do the same in 
> chimera.> How to draw these spheres? I tried to find it in the 
> guide book but did not see anything. Probably missed it.
> > Thank you so much for your help,
> > Roni
> > 

Roni Rayes (BS, MS)

Graduate Research Assistant
Institute of Molecular Biophysics
Florida State University
91 Chieftan Way
Tallahassee, Fl 32306
Phone # (850) 645-1335
Fax # (850)644-7244

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