Capping a clipped sphere representation
Hi, I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible? I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing. Thanks for your help, Michelle
Hi Michelle, Sorry, Chimera doesn't have capping of atomic representations or ribbons. However, you can achieve something similar to the "sliced spheres" by: (a) showing a molecular surface (b) clipping and capping that surface (capping occurs by default) (c) coloring the molecular surface to match the atoms (this occurs by default) (d) the nonobvious step: coloring the cap to match the atoms too, using Color Zone See the picture here to get some idea if this will meet your needs: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> It sounds like you figured out (a)-(c). Then open Color Zone (under Tools... Volume Data), select the protein atoms (for example, command "sel protein"), click "Color" on the Color Zone tool to color the MSMS surface (which includes the cap). Radius values >2.5 should all be fine, the closest atom is used. However, at this point the coloring may look jagged. You could use a finer triangulation of both the molecular surface and the surface cap to make the former smoother, and get rid of jagged coloring edges in both. There are several ways of increasing the vertex density of a molecular surface, but the easiest to describe in email is this command: setattr s density 5 ... where the default density is 2. You could try different numbers, being aware that finer triangulations (higher density values) use more memory and may make rotating the structure slower. To get a finer triangulation of the cap, start Surface Capping, for example by clicking the "Surface capping..." button in the side view, and increase the "Mesh subdivision factor," say to 3. Several of these steps are also covered in the "B-factor coloring" image tutorial. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> 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 Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote:
Hi, I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible?
I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing.
Thanks for your help, Michelle
Hi Michelle, If you're willing to use an image that is just atom spheres, i.e. no surfaces, volumes, BILD objects, etc. then you can use the "conic" command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/conic.html It will produce an image like the one I've attached. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 24, 2011, at 6:50 PM, Elaine Meng wrote:
Hi Michelle, Sorry, Chimera doesn't have capping of atomic representations or ribbons. However, you can achieve something similar to the "sliced spheres" by:
(a) showing a molecular surface (b) clipping and capping that surface (capping occurs by default) (c) coloring the molecular surface to match the atoms (this occurs by default) (d) the nonobvious step: coloring the cap to match the atoms too, using Color Zone
See the picture here to get some idea if this will meet your needs: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html
It sounds like you figured out (a)-(c). Then open Color Zone (under Tools... Volume Data), select the protein atoms (for example, command "sel protein"), click "Color" on the Color Zone tool to color the MSMS surface (which includes the cap). Radius values >2.5 should all be fine, the closest atom is used.
However, at this point the coloring may look jagged. You could use a finer triangulation of both the molecular surface and the surface cap to make the former smoother, and get rid of jagged coloring edges in both.
There are several ways of increasing the vertex density of a molecular surface, but the easiest to describe in email is this command: setattr s density 5 ... where the default density is 2. You could try different numbers, being aware that finer triangulations (higher density values) use more memory and may make rotating the structure slower.
To get a finer triangulation of the cap, start Surface Capping, for example by clicking the "Surface capping..." button in the side view, and increase the "Mesh subdivision factor," say to 3.
Several of these steps are also covered in the "B-factor coloring" image tutorial. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html
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 Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote:
Hi, I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/ atom to be capped and colored the same color as the atom. Is this possible?
I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing.
Thanks for your help, Michelle
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The "conic" command was exactly what I was looking for! I ended up using the command: conic -s -f ps -o test.ps Thanks so much for your help, Elaine and Eric! Michelle On Sun, Jun 26, 2011 at 5:56 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Michelle, If you're willing to use an image that is just atom spheres, i.e. no surfaces, volumes, BILD objects, etc. then you can use the "conic" command:
http://www.cgl.ucsf.edu/**chimera/current/docs/** UsersGuide/midas/conic.html<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/conic.html>
It will produce an image like the one I've attached.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 24, 2011, at 6:50 PM, Elaine Meng wrote:
Hi Michelle,
Sorry, Chimera doesn't have capping of atomic representations or ribbons. However, you can achieve something similar to the "sliced spheres" by:
(a) showing a molecular surface (b) clipping and capping that surface (capping occurs by default) (c) coloring the molecular surface to match the atoms (this occurs by default) (d) the nonobvious step: coloring the cap to match the atoms too, using Color Zone
See the picture here to get some idea if this will meet your needs: <http://www.cgl.ucsf.edu/**chimera/docs/UsersGuide/** tutorials/bfactor.html<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
It sounds like you figured out (a)-(c). Then open Color Zone (under Tools... Volume Data), select the protein atoms (for example, command "sel protein"), click "Color" on the Color Zone tool to color the MSMS surface (which includes the cap). Radius values >2.5 should all be fine, the closest atom is used.
However, at this point the coloring may look jagged. You could use a finer triangulation of both the molecular surface and the surface cap to make the former smoother, and get rid of jagged coloring edges in both.
There are several ways of increasing the vertex density of a molecular surface, but the easiest to describe in email is this command: setattr s density 5 ... where the default density is 2. You could try different numbers, being aware that finer triangulations (higher density values) use more memory and may make rotating the structure slower.
To get a finer triangulation of the cap, start Surface Capping, for example by clicking the "Surface capping..." button in the side view, and increase the "Mesh subdivision factor," say to 3.
Several of these steps are also covered in the "B-factor coloring" image tutorial. <http://www.cgl.ucsf.edu/**chimera/docs/UsersGuide/** tutorials/bfactor.html<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
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 Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote:
Hi,
I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible?
I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing.
Thanks for your help, Michelle
______________________________**_________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi everybody, Is there a way to put only polar hydrogens on a protein structure with chimera? Regards, Luis L.
Hi Luis, No, but after adding all hydrogens, you can delete the "nonpolar" ones if you really don't want them. This could be done with the command: delete HC ...or equivalently with menu operations: Select... Chemistry... IDATM type... HC Actions... Atoms/Bonds... delete 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 Jun 28, 2011, at 1:25 PM, lecan wrote:
Hi everybody, Is there a way to put only polar hydrogens on a protein structure with chimera? Regards, Luis L.
participants (4)
-
Elaine Meng -
Eric Pettersen -
lecan -
Michelle E. McCully