[Chimera-users] drawing spheres with various radii

[Tom Goddard]

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
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