[Chimera-users] Capping a clipped sphere representation
Michelle E. McCully
mmccully at uw.edu
Mon Jun 27 14:44:20 PDT 2011
The "conic" command was exactly what I was looking for! I ended up using
conic -s -f ps -o test.ps
Thanks so much for your help, Elaine and Eric!
On Sun, Jun 26, 2011 at 5:56 PM, Eric Pettersen <pett at 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:
> It will produce an image like the one I've attached.
> 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
>> (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:
>> 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
>> I hope this helps,
>> 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:
>>> 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
>>> Thanks for your help,
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
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