[Chimera-users] drawing spheres with various radii

[Roni Rayes]

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,

Roni

----- 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
> 
> Tom
> 
> > 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.
> >> 
> <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
> > _______________________________________________
> > 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