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