[Chimera-users] drawing spheres with various radii

[Elaine Meng]

Also, all these options are described on the "shape sphere" manual page (follow the link in my previous message).
Elaine

On Nov 3, 2010, at 11:37 AM, Tom Goddard wrote:

> 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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>> 
> 
> 
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