[Chimera-users] drawing spheres with various radii
rfr06 at fsu.edu
Wed Nov 3 11:52:32 PDT 2010
Thank you so much for your help.
Got it to work. I was creating the sphere and then trying to center it and change its radius.
We should specify radius, center and color whiel creating it!
That was the catch :)
Thanks again Tom & Elaine,
----- Original Message -----
From: Tom Goddard <goddard at sonic.net>
Date: Wednesday, November 3, 2010 2:37 pm
Subject: Re: [Chimera-users] drawing spheres with various radii
To: Roni Rayes <rfr06 at fsu.edu>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Hi Roni,
> Here's an example shape command to make a sphere of radius 25
> Angstroms, centered on the CA atom of residue 123 of chain B of
> model #0
> with color transparent yellow (red = 1, green = 1, blue = 0,
> opacity =
> 0.5) and in "mesh" style.
> shape sphere radius 25 center #0:123.B at CA color 1,1,0,0.5 mesh true
> > 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 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.
> >> 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
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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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