[Chimera-users] drawing spheres with various radii

Roni Rayes rfr06 at fsu.edu
Wed Nov 3 10:56:15 PDT 2010

Thank you so muck for your help Elaine.

shape sphere works fine for me.
Now need to find out how to change radius, center,...

Will try and let you know.


----- 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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