drawing spheres with various radii
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
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
Thank you so muck for your help Elaine. shape sphere works fine for me. Now need to find out how to change radius, center,... Will try and let you know. 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
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
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@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@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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@sonic.net> Date: Wednesday, November 3, 2010 2:37 pm Subject: Re: [Chimera-users] drawing spheres with various radii To: Roni Rayes <rfr06@fsu.edu> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@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@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@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 _______________________________________________ Chimera-users mailing list Chimera-users@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
participants (3)
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Elaine Meng -
Roni Rayes -
Tom Goddard